Gamepad Issue: If happens that you want to play with a gamepad (Generic, Xbox, etc...) and does not respond besides being plugged in and seeing that other games respond to the gamepad right, try closing Steam, or logging out. It may be "stealing" your #ClickteamFusion controller inputs for the Steam Input in some games. Otherwise, restarting the PC should be fine as well.

This really gave me a bad headache. Also thought I had to remap all the buttons, all over again.