I'm not seeing any alignment issues with the latest on master. See the srtp_driver output below, which is from an Android ARM device. I used the Android NDK to build libsrtp, which is using gcc 4.8. Since this issue has been open for a long time, I'll close the issue for now. Please re-open the issue if a recreate procedure can be provided.

[foleyj@firedragon libsrtp]$ arm-linux-androideabi-gcc --version
arm-linux-androideabi-gcc (GCC) 4.8
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

shell@grouper:/data/local/tmp $ ./srtp_driver
usage: ./srtp_driver [ -t ][ -c ][ -v ][-d <debug_module> ]* [ -l ]
-t run timing test
-r run rejection timing test
-c run codec timing test
-v run validation tests
-d turn on debugging module
-l list debugging modules
1|shell@grouper:/data/local/tmp $ ./srtp_driver -v
testing srtp_protect and srtp_unprotect

SSRC: any outbound

rtp cipher: null cipher

rtp auth: hmac sha-1 authentication function

rtp services: authentication

rtcp cipher: null cipher

rtcp auth: hmac sha-1 authentication function

rtcp services: authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect with encrypted extensions headers

SSRC: any outbound

rtp cipher: null cipher

rtp auth: hmac sha-1 authentication function

rtp services: authentication

rtcp cipher: null cipher

rtcp auth: hmac sha-1 authentication function

rtcp services: authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: 1

testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect_rtcp and srtp_unprotect_rtcp

SSRC: any outbound

rtp cipher: null cipher

rtp auth: hmac sha-1 authentication function

rtp services: authentication

rtcp cipher: null cipher

rtcp auth: hmac sha-1 authentication function

rtcp services: authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: null authentication function

rtp services: confidentiality

rtcp cipher: aes integer counter mode

rtcp auth: null authentication function

rtcp services: confidentiality

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing that ciphertext is distinct from plaintext...passed
passed

testing srtp_protect and srtp_unprotect with encrypted extensions headers

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: null authentication function

rtp services: confidentiality

rtcp cipher: aes integer counter mode

rtcp auth: null authentication function

rtcp services: confidentiality

window size: 128

tx rtx allowed:false

Encrypted extension headers: 1

testing that ciphertext is distinct from plaintext...passed
passed

testing srtp_protect_rtcp and srtp_unprotect_rtcp

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: null authentication function

rtp services: confidentiality

rtcp cipher: aes integer counter mode

rtcp auth: null authentication function

rtcp services: confidentiality

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing that ciphertext is distinct from plaintext...passed
passed

testing srtp_protect and srtp_unprotect

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing that ciphertext is distinct from plaintext...passed
testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect with encrypted extensions headers

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: 1

testing that ciphertext is distinct from plaintext...passed
testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect_rtcp and srtp_unprotect_rtcp

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing that ciphertext is distinct from plaintext...passed
testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect

SSRC: any outbound

rtp cipher: null cipher

rtp auth: null authentication function

rtp services: none

rtcp cipher: null cipher

rtcp auth: null authentication function

rtcp services: none

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

passed

testing srtp_protect and srtp_unprotect with encrypted extensions headers

SSRC: any outbound

rtp cipher: null cipher

rtp auth: null authentication function

rtp services: none

rtcp cipher: null cipher

rtcp auth: null authentication function

rtcp services: none

window size: 128

tx rtx allowed:false

Encrypted extension headers: 1

passed

testing srtp_protect_rtcp and srtp_unprotect_rtcp

SSRC: any outbound

rtp cipher: null cipher

rtp auth: null authentication function

rtp services: none

rtcp cipher: null cipher

rtcp auth: null authentication function

rtcp services: none

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

passed

testing srtp_protect and srtp_unprotect

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing that ciphertext is distinct from plaintext...passed
testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect with encrypted extensions headers

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: 1

testing that ciphertext is distinct from plaintext...passed
testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect_rtcp and srtp_unprotect_rtcp

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing that ciphertext is distinct from plaintext...passed
testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect

SSRC: any outbound

rtp cipher: null cipher

rtp auth: hmac sha-1 authentication function

rtp services: authentication

rtcp cipher: null cipher

rtcp auth: hmac sha-1 authentication function

rtcp services: authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect with encrypted extensions headers

SSRC: any outbound

rtp cipher: null cipher

rtp auth: hmac sha-1 authentication function

rtp services: authentication

rtcp cipher: null cipher

rtcp auth: hmac sha-1 authentication function

rtcp services: authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: 1

testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect_rtcp and srtp_unprotect_rtcp

SSRC: any outbound

rtp cipher: null cipher

rtp auth: hmac sha-1 authentication function

rtp services: authentication

rtcp cipher: null cipher

rtcp auth: hmac sha-1 authentication function

rtcp services: authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect with big policy

SSRC: 0x00000000

rtp cipher: null cipher

rtp auth: hmac sha-1 authentication function

rtp services: authentication

rtcp cipher: null cipher

rtcp auth: hmac sha-1 authentication function

rtcp services: authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

SSRC: 0x01000000

rtp cipher: aes integer counter mode

rtp auth: null authentication function

rtp services: confidentiality

rtcp cipher: aes integer counter mode

rtcp auth: null authentication function

rtcp services: confidentiality

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

SSRC: 0x02000000

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

SSRC: 0x03000000

rtp cipher: null cipher

rtp auth: null authentication function

rtp services: none

rtcp cipher: null cipher

rtcp auth: null authentication function

rtcp services: none

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

SSRC: 0x04000000

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

SSRC: 0x05000000

rtp cipher: null cipher

rtp auth: hmac sha-1 authentication function

rtp services: authentication

rtcp cipher: null cipher

rtcp auth: hmac sha-1 authentication function

rtcp services: authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect with big policy and encrypted extensions headers

SSRC: 0x00000000

rtp cipher: null cipher

rtp auth: hmac sha-1 authentication function

rtp services: authentication

rtcp cipher: null cipher

rtcp auth: hmac sha-1 authentication function

rtcp services: authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

SSRC: 0x01000000

rtp cipher: aes integer counter mode

rtp auth: null authentication function

rtp services: confidentiality

rtcp cipher: aes integer counter mode

rtcp auth: null authentication function

rtcp services: confidentiality

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

SSRC: 0x02000000

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

SSRC: 0x03000000

rtp cipher: null cipher

rtp auth: null authentication function

rtp services: none

rtcp cipher: null cipher

rtcp auth: null authentication function

rtcp services: none

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

SSRC: 0x04000000

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

SSRC: 0x05000000

rtp cipher: null cipher

rtp auth: hmac sha-1 authentication function

rtp services: authentication

rtcp cipher: null cipher

rtcp auth: hmac sha-1 authentication function

rtcp services: authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: 1

testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect on wildcard ssrc policy

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: none

testing that ciphertext is distinct from plaintext...passed
testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect on wildcard ssrc policy and encrypted extensions headers

SSRC: any outbound

rtp cipher: aes integer counter mode

rtp auth: hmac sha-1 authentication function

rtp services: confidentiality and authentication

rtcp cipher: aes integer counter mode

rtcp auth: hmac sha-1 authentication function

rtcp services: confidentiality and authentication

window size: 128

tx rtx allowed:false

Encrypted extension headers: 1

testing that ciphertext is distinct from plaintext...passed
testing for false positives in replay check...passed
testing for false positives in auth check...passed
passed

testing srtp_protect and srtp_unprotect against reference packets
passed

testing srtp_protect and srtp_unprotect against reference packets with encrypted extensions headers
passed

testing srtp_protect and srtp_unprotect against reference packets (AES-256)
passed

testing srtp_protect and srtp_unprotect against packets with empty payload
passed
testing srtp_remove_stream()...passed
testing srtp_update()...passed

from libsrtp.