I can not help much with the USB problem, but I would store my projects in a directory some place other than a sub directory of PBP. C:\projects woud be good. Most of my projects are on a flash drive or a SD card to make it easy to move from machine to machine.

When you have projects in the PBP ditectory and it comes time to upgrade them you will have to go find all of your "stuff" before it is deleted or over written during the new install.