Yep, did it. Nothing.
I've tried many times now, with more than one virtual drive enabled, and only once (with 2 enabled) on the second virtual drive it worked. Only once though, I could not replicate it again no matter what settings I moved around. Tried muxing bluray and m2ts, muxing everything, muxing only one video and one audio, and nothing.
I'm trying two movies right now. Shinobi and Before the Devil Knows you're Dead. The one time it worked was with Shinobi. This movie is giving me a message that it cannot read one stream (the japanese language lossless track), so it doesn't show up in tsmuxer. The English lossless track is detected OK. The time it worked, though, the Japanese track was also detected OK, so this might be related. I don't know what else I can try.
It also fails with AnyDVD enabled with an ISO of There Will Be Blood, but that ISO is unprotected, I accidentally ripped it with AnyDVD enabled. If I disable AnyDVD for that ISO it does mux OK as expected. I'll be ripping it again with AnyDVD disabled just to check another disc, I'll see how it goes.