Are all the files this happens on .mkv files?
After version 1.52.1 something happened either to PMS or to mencoder which is packaged with it. It seems that mencoder jumps to 100% CPU utilization near the end of playback.
There are two ways to "fix" this ... either force close all mencoder instances near the end of each video. Or roll back to version 1.52.1 where this working. Go here to download version 1.52.1 ... https://code.google.com/p/ps3mediaserve ... 1&q=1.52.1