Quite recently I have faced this situation with the MKV files I use to stream or play, via usb interface or via DVD holding the 3D MKV and subtitle files. They do not play as they should.
In my case I was using my LG BD390 player, through which I stream and play all my MKV files, with no problem at all. Put srt file on the same folder or merge them together.
For the sub files, I converted the srt to 3D subs with 3DSubtitler, but I can't seem to play them.
Now I'm researching on other players, like the Oppo BDP-103, which is also 3D, to see if it can play this I'm asking.
Can anyone comment on their experience?