Strange audio delay - 2 identical streams one is OK one is shifted

[IcePlanet]

After last help all encoding run without any problems. But now I encountered strange problem. Have 2 recordings (.ts), made from the same stream and 24 hours apart, each recording has 2 audio tracks. Encoding settings identical on both recordings and on both tracks. 3 tracks are perfectly in sync, but 4th track is out of sync.

Video 1 audio track 0 is out of sync
Video 1 audio track 1 is in sync
Video 2 audio track 0 is in sync
Video 2 audio track 1 is in sync

The sync is almost precise at beginning of output file, and 1.5s at the end. The bad thing is that I can not replicate on small block of the file.

Media info from the original .ts

MPEG Audio Version 1 Layer 2 Constant 160 kb/s 160 kb/s

Media info from the resulting .mkv

AAC LC SBR PS HE-AACv2 NBC A_AAC-29 2 channels

Attached is .py script for both encodings and Media Info from all 4 files (2x original, 2x result).