Disappearing mates in SW 2007

I'm working on an assembly of 20-30 fairly simple parts. The assembly includes a part with a master sketch that is extremely large. I model the parts without external references for the most part. I mate them into the assembly, save the assembly, close Solidworks, re-open the assembly, resolve everything, rebuild everything and everything's fine. I do this more than once. I go home. This morning when I opened the assembly, dozens of mates were broken, always because a surface on a part was not recognized. Any ideas what may be causing this in SW 2007 sp 2.1? Thanks,