I don't use the Juke Box, but from your statement regarding 'Real Tracks the laptop doesn't have space for', I would guess that is the root of your problem. If you have the usb (external) drive version of BIAB see if you can play the songs from there on the laptop by running BIAB from the usb drive as well. BIAB doesn't embed the RTs as far as I know, so they need to be on the computer running BIAB. As for messing up other programs, if the laptop is a bit old and the drive is getting full you might have some bad sectors and/or cross-linked sectors going on. You might try running some diagnostics on the hard drive.
Good luck.