It seems to cause problems with VLC, MPC-HC, VirtualDub2, and possibly ffmpeg itself - whether it's in MKV or TS - but happily it doesn't affect my TV, apart from perhaps a very slight stutter on the transition.
So I use DGIndexNV to output a trimmed TS, use MKVToolNix to repack it to an MKV, then use ffmpeg to reencode audio only to AC3.
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