I bought a Wii U pro controller that isn't a knockoff, and it works properly. I thought desyncing it from the Wii U would fix my problem but no. You can tell if you have an official pro controller created by Nintendo by seeing a Wii U logo at the top of the controller. I hope this helps anyone else with problems.
Yeah, that is the case. Unfortunately I haven't found any information on if there is a way to bypass this. You haven't happened to try using the Sync button inside WiinUPro/Soft with the Microsoft Stack have you?