mmodri: I'm using a cheap knockoff ps2/ps3 controller that doesn't support xinput and it works without any special software with Freedom Planet, have you tried playing it without DS4Windows?
tbonekenny: I have and with or without DS4Windows it will now only work when plugged in via USB and not wireless.
I see, it could be something to do with the wireless drivers or the xinput.dll that comes with freedom planet is somehow messing with your controller. You could try asking on the official FP forums, there's a bunch of active posters there, someone must know whats up.