I had to reinstall my desktop PC (running Ubuntu) and ever since PMS has played all my MTS files in double speed. I traced this to the fact that parameter -ofps 50 is passed to mencoder when transcoding the file. Before the reinstallation the parameter was passed as -ofps 25.
Now, All I need to know is how, where or with what PMS detects the fps of any particular file so that I can fix this issue.
EDIT: Solution was to install mediainfo and libzen, both of which were missing. Apparently PMS uses ffmpeg if those are not found and ffmpeg seems to be unaccurate.