When the unit locks up are there any lights lit on the controller? We had a cFP-2010 and backplane that would shutdown after 30 to 60 minutes running proven code. Was completely unresponsive and had no lights at all, just as if it was unplugged. Cycling power brought the unit right backup. Problem was specific to that controller and backplane combination.
I agree with Ben, though, certainly sounded like memory. Are you allocating memory in process, so that maybe even though there is plenty of memory there is not a large enough chunk available?
Matt