Well, I didn't even think to unplug the joystick, it's nothing that amazing, but sure enough, it's the bloody new stick. Looks like it's a conflict with the default MS HID-compliant game controller drivers, I just need to figure out how to uninstall them so I can put the proper divers in their place. (it seems FS X has the same issue with this stick)
Thanks for your help Vohk, I shall just pray to you next time!