I did some more testing of 3D ISOs in TMT5 this weekend. Most of the time when playing the ISO it would begin in 3D and then revert to 2D (usually within 2 minutes -- mostly didn't even get through the promos). Trying to toggle 2D to 3D didn't work. However, simply stopping the movie, and then restarting it again would get 3D stable and working correctly. These are full clone ISOs mounted with VCD. I don't experience this kind of issue with the actual discs.
Hope this info can help. Stop, then restart worked every time.