PC repair shops are notorious for stealing data and worse (particularly but not limited to Best Buy). Consider anything that wasn't encrypted or that could be opened even though encrypted with the account information that you gave them to be compromised. I'm not sure why they felt they had to use knoppix if you gave them a user and password, but maybe they were just being thorough in their snooping.

On top of it all, you likely paid them a small fortune to undo 4 screws and replace the power supply, as well as snoop around on your system. You could have easily swapped the power supply yourself.