I recently also had a problem where PMS worked fine and stopped after a min or two, fast forward automatic skipping, etc.
After trying all sort of things I could find in the forum (MEncoder update, bigger java heap size, bigger buffer, turning off settings and playing with all sorts of settings) nothing really helped. The only thing that helped is that I noticed I had multiple java versions installed. I had the latest 7 ver update 11 and also update 10. I started by uninstalling PMS and removed the conf file from the All Users/PMS/pms.conf location. Just to make sure it'll use a new one on reinstall. Then I removed all the java installations I had and installed only the latest one for both x64 and x32 bit. (I use Win7 x64 so its best to have both). Then installed PMS and didn't really need to change anything. Transcoding is now perfect without any crashes and sudden halts.
*Edit , works only when not using PMS as a server and when FFmpeg transcoding is used instead of MEncoder. Otherwise on some files it still exit after a few mins.