I have a similar issue.... can you check task manager on your server and look for the service NMService.exe...
Watch the memory usage for this applet... mine gradually rises with users accessing the website and the console... memory is grabbed and never released...
When left over night by the time the next day has come the WUP Pro application has fallen over and required a stop/start and the sequence starts again..
I think it is a memory leak in one of the new dll's posted by SP1... the other day this NMService.exe application was using 1.2G on RAM..