Trashing Prefs is always worth a try for any odd behavior. Since doing the cleaning seems to be the cause, that would be my first thing to check(re-seat all cards, RAM and connectors in the tower). Next thing that can wreak havoc is if drive letters change(and they can change if any single drive is not read on a boot-up). If you know what drive letter belongs to every drive, check that they are all correct. If you don't remember, once you get things working again(fingers crossed), write the drive letters on a Post-It and stick it to the side of the tower
