Hi nozuul and thanks for the kind words.
AVStoDVD uses the capability of FFMpegSource to select different audio tracks than the main one (track 0). If you choose track 0, then it is likely that DirectShowSource will be used, instead if you choose track 1, 2, etc. than FFMpegSource is called.
There should be some fights between FFMS and your m2ts files. If you can, send me a short sample of the m2ts.
A quick try you can alway do is to launch Preview Clip before starting to encode.
Bye