First, I must say I love PS3 Media Server. It's the first solution I've found that doesn't suck.
I recently encountered a problem where, when playing a transcoded mkv file on my PS3, the subtitles would extend off the screen if there were multiple lines of text, making them almost unreadable. The same video played on my PC with VLC media player showed the subtitles correctly.
I am running PMS 1.72.0 on Windows Vista, using MEncoder with default settings for the transcoding.
Appreciate any assistance. I'm not terribly knowledgeable when it comes to video formats and transcoding as such, so if I've left out any pertinent information, please let me know.