I have recently been running into a problem with my large assemblies. I build utility and fire rescue bodies so my assemblies grow quite large. However, the problem I've been having lately is after I save and close an assembly if I go to reopen it later the majority of the parts are "lightweight" and half of my mates are either suppressed or creating over definitions. Any clues?
Go to your system options, then performance and assemblies. Check your large assembly settings, and lightweight settings. I'm guessing if you change some of those you won't get the parts loading lightweight. Not sure on your mate errors. Does a ctrl-q rebuild help?