There's no reason I can think of as to why the GP-Wiz49 should not be working with your new build, unless the sticks aren't getting their required 5VDC and GROUND, or your new installation hasn't enabled the joystick option.
What happens in the gaming devices test screens of the OS?
*edit*
If the issue is specific to front-end navigation, either the FE you are using doesn't support joystick navigation, or there is a setting which needs to be enabled for it.