For Spenzz, I had the same irritating problem. I had a USB to Playstation controller adapter connected, so regardless of keyboard or joystick, I still think it's the same problem. It was a pain, but I got it to work, I don't really remember how though. I went into PAD 2 and it worked fine there, saved the settings and hit OK and then I went back into PAD 1 and it actually let my button presses stay. I think I may have done that, just "fiddle farting" around with it a few times (all the time, wondering what the heck was going on

). But it worked that one time, so there is hope, just keep trying and good luck.