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Unfortunately the controller support is a bit spotty, especially on non-Windows platforms, and there is very little I can do to help. People who came up with ways of emulating the 360 pad under Linux were able to get their controllers to work, but not being a Linux guy, I wouldn't be able to say how.

I have long been working on an update to the game that may solve this issue, as well as a whole bunch of other ones (60 fps, larger play window, optional 4:3 mode, turbo-speed, better controller support, redefine keys menu, better game balance etc). Hopefully I'll be able to release it sometime soon.

Those updates sound good. The workaround I've found is using AntiMicro to remap the keyboard keys to my pad but it would make the game harder to play for my HTPC setup. I'll look forward to the update.