I did in fact think to reconfigure the controller settings after posting that and it now works fine.
How do I go about modifying the zc.cfg file? I don't want to mess around with that unless I know what I'm doing.
Fullscreen works in Classic, I haven't tried it in ZQuest yet. The quest I and my friend are putting together is still in the planning stages and we have more work to do before we are ready to put it together in ZQ. I am running Windows 8.1 with default drivers so I couldn't tell you anything about Win 7 or other drivers.
UPDATE: ZQ won't open if set to fullscreen, or if the window scale us set to anything besides x1. It will still open in the original size window, however.