My configuration:
Windows 7 64 bit, ConvertXtoVideo 1.6.0.4
When I remux an MTS file (1920x1080 50p), glitches appears on the top of the picture. When I use tsMuxeR or MultiAVCHD, there are no glitches.
I tested the resulted bluray disc in a Samsung BD-H6500 player and the audio is out of sync. When I tested with PowerDVD, the audio is OK.
No improvements. From internal tests done when we updated FFMPEG the support for this file got even worse, we corrected that so that the file would convert with the same bug as you reported but the initial bug still requires a fix but I think it might not be that simple otherwise it would have been done with we corrected the internal regression when we updated FFMPEG.