Like you see FFMS2 can have problems with TS files.
Using MeGUI with your original sample I recommend this:
1) Open the E:\sample\sample.ts with MeGUI -> Tools -> HD Streams Extractor (eac3to GUI)
2) Extract the video track as MKV (if you want resize/recode the MKV with FFMS2)
3) Extract/decode the track 3 (the desired MP2, audio track 2) like WAV
4) Open the WAV with MeGUI Input Audio and recode the WAV to your desired format (if you want low quality aac -he 64 Kb/s use Qaac instead NeroAacEnc)
5) Mux with MeGUI -> Tools -> Muxer -> MKV Muxer the video and audio.
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BeHappy, AviSynth audio transcoder.
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