Not to bump this, but this is the most relevant thread for my problem.
I'm having the exact opposite problem. I'm playing back video and no subtitles are appearing when they should be. One file plays back the opening with subs, but I'm assuming that appears to be hard-subbed into the file while the subtitles for the dialog seem never appear, as if Subtitles are turned off for that particular .MKV file.
edit: I think I found it for some reason, the PS3/Media Server wasn't recognizing that the ASS/SSA Subtitles option was checked or maybe they weren't communicating it right. Well.. no.. that doesn't seem to fix it either. *goes back to tinkering*