I didn't fix the crashing but I fixed the sync problem by:
extracting the h264 from the m2ts (wouldn't work other wise
)
Creating a dga file index file and then loading it with
LoadPlugin("DGAVCDecode.dll")
AVCSource("00001.track_4113.dga")
Works perfect for me now.
I'll have to test around with different sources to see what was crashing ffms2 and if it still happens I'll post an example of the source.