Hi Ben,
It is not possible to have reprogrammed the PIC over USB. Try rebooting the computer and power cycling the board to see if that resolves the issue. If you are still having problems, ensure NI-Visa is installed and that no other versions of Visa (aka TekVisa or AgilentVisa) are installed. It is is also possible USB development tools could be interfering with your USB port. Ensure that debuggers are not running in the background and that you can see the ADI driver in your device manager. We do not recommend plugging the evaluation boards into a hub or cables longer than 6ft.
-Michael