I wasn't able to test my rip on my system, only my relatively slow laptop. However, it was obvious my sync was way off: I didn't use an offset.
I haven't ripped a 3D Blu-ray before so a bit of trial and error. I re-ripped last night with DVD Fab instead, and it looks like a nice .m2ts is waiting for me when i get off of work to play with.
I do still want to figure out how to get that old universal logo on there eventually too.