You can force a rescan of the blockchain, which will als build a new database. It's likely that your database is synced to your fresh wallet or that your old wallet's database was corrupted in some other fashion. Basicly, just back up your wallet.dat files and then choose the rescan option in the menu.
I seriously can't figure out how to do that. Been trying to figure that out for hours now. Could you please be very specific on how to do this?
Not really, I havn't used the standard client in months. But I've done it before, I just can't remember how. Also, it's unlikely that your system would act like mine, assuming you use M$ Windoze.