I have no clue about how to fix your computer/blackberry problem directly. However one solution for syncing is to use the Google mobile app. I use it now and can sync my calender, contacts and settings going both ways. It's not a solution to your problem as such, but perhaps a help for a new way to back everything up and minimize mounting your BB on the PC until you figure out why you're SOL.
One bonus; after you have a problem, or switch phones, backup can be done over the air.