Audio playing fine in VLC, but missing in Aegisub

[yami]

I don't know, if this actually is related to the encoding of the ts or rather a bug in Aegisub... But I need to narrow the issue down. It's a small part just before the end of the encoded raw, about 10 seconds, where suddenly the audio is gone in Aegisub, and then appears again. In VLC, the audio plays through fine. I have had this issue before with other tsses, but it is... time to tackle this, I feel. Is there a way to be cutting a sample from a ts out of somwhere in its middle?
I am using the latest Nightly on Max OS 10.8.5 on a MacBook Pro, but the issue has been there before, with older 2.6 releases of Avidemux.
The raws are encoded as mkv with the Audio as 'Copy', stream is mpeg2/AAC

Audiostream of ts by VideoSpec:
Audio
ID : 272 (0x110)
Menu ID : 33840 (0x8430)
Format : AAC
Format/Info : Advanced Audio Codec
Format version : Version 2
Format profile : LC
Muxing mode : ADTS
Codec ID : 15
Duration : 30mn 25s
Bit rate mode : Variable
Bit rate : 192 Kbps
Channel(s) : 2 channels
Channel positions : Front: L R
Sampling rate : 48.0 KHz
Compression mode : Lossy
Stream size : 41.8 MiB (1%)

[yami]

To clarify a bit of the problem: I actually can't share the ts (it's 3 GB anyways - which is, why I asked, if there is a way to make a sample from the further end of the ts), the encoded and cut raw as mkv is here: https://mega.co.nz/#!v1QlmYKC!e9l_eD_TYZgLma71x8HHBH0oEPp2eA8uc3vZX8VZar8
The encode was done with Avidemux, Audio on 'copy'. It may be connected to issues with the audio of original ts that Avidemux doesnt manage to adress, as ts-ses from other broadcasters don't show this after encoding...
Here are screenshots: (1) https://mega.co.nz/#!nlgSTJ5A!earUJHY3adh1mGvLezq9pTGjhv8mln_NYq0yzRyr89Q and (2) https://mega.co.nz/#!2w4UAYwQ!S9qGdVBHlWBm59EhD59wDHgJ2G9PSFDZI5u3umYC_HY
The place, where the ads after the ED were cut out is at roughly 23:49.87, at 24:01.79 the audio disappears (1) and a bit later, it's just back (2) around 24:15.89 - ish, the last set of ads was trimmed off after the final credits.