I've run into a problem like this before too -- fast-forwarding, rewinding, and sometimes even pausing a video causes the video to black-out, return an error, or exit. And restarting the video at the point I left off isn't always possible; I have to start the video over again, fast-forward, and then stop fast-forwarding right before hitting the "problem" part of the file. If I hit the "problem" part of the video then it exits again. The "problem" part of the video varies -- but it's usually around some point near the end of the video -- well, in the last 1/3 of the video.
However, for me, this has only happened with particular videos (and only with videos that are in RAR format) -- I can play a couple of dozen RAR videos before encountering the problem. But when I do run into the problem it can be consistently repeated with that particular video. So I've always figured that these rare instances are related to a corrupted RAR file and not Boxee's fault. (Maybe.)
The newer problem I'm having is affecting ALL of the RAR files on my iMac. I can't get them to play on the Boxee Box at all anymore, unless I un-RAR them first or move the RAR files over to my NAS. This used to work, but stopped working after I upgraded to Boxee firmware 1.2 and OS X Lion and switched to AFP instead of SMB. Frustrating. For details, see: http://forums.boxee.tv/showthread.php?p=208110#post208110