I have tested this extensively using the original disc, here are the results:
MP4+encode Audio to AAC=perfect sync
MP4+Copy Audio=perfect sync
MP4+encode audio+deinterlace=perfect sync
MKV+Copy audio=bad sync error, >2 seconds
MKV+encode audio to AAC=perfect sync
So, for now you can use the MP4 format with any settings for a perfect rip, or use MKV and encode the audio to AAC.
I am sure it can be fixed, but until it is you have some alternatives. MP4 is more universally playable the MKV in any event.