Compressor on FCS 2 "hiccups" when encoding MPEG-2 files

I have had numerous instances where Compressor simply "hangs" or "hiccups" when encoding MPEG-2 files (and sometimes the AC 3 files, but less frequent). Although I empty the Preference/p-list files, this problem seems to re-surface. In order to save time while trying to find a solution, I will copy the finished file (which appears "hung" by Compressor), so the finished work will not be erased when resuming to the next file. Does anyone have a possible solution? I am losing precious time when having batches of files schedules to run overnight, and find myself having to start over again and again.