It's not that the subtitles disappears behind objects as that's not possible, but they appear at the wrong depth compared to some items that pops out of the screen, giving them a really weird and eye-hurting effect as they appear further away than what's behind them.
If you have ever inverted the 3D on your TV/projector/monitor making things that's further away closer and vice versa, it looks like that but only for the subtitles.
Oops, I'm using DVDFab 10.0.2.8.
Another thing I just noticed is that DVDFab does not preserve subtitle position when converted to 3D, while BD3D2MK3D does so.
Example:
Left is DVDFab and right is BD3D2MK3D.
It's not something that's super necessary but I have come across some 2D movies that uses subtitles for non-English title cards and such, (for example Inglorious Basterds) which could be messed up if it was converted to 3D or released as a 3D movie.