Yes, the only two streams I leave in TSMuxer-created m2ts are H.264 video and downconverted TrueHD. I have seen Handbrake "stall" on 3 titles created this way.. but it works fine when there is an "native" AC3 in the title.
I haven't tried it with any pre-0.93 versions, perhaps something peculiar to this release. Next time I encode TrueHD title and see this issue - I will capture Handbrake debug and post on HB forums.
I think this is the problem I'm running into.
I TSMuxed 5th Element and the windows version of handbrake 0.93 is just hanging out forever. It's been about 30 minutes so I'll give it a bit longer and see what happens.