What buttons don't work?
Did you try to reconfigure it (e.g., click on the "Clear Controller" button and then reconfigure it)?
I haven't play'd with mouse control in about seven month's (and I don't like it).
And I hate to say, buy a gamepad, mine only cost $29, it's much better than a mouse, but a mouse is better then just a keyboard!
Just a keyboard is only good for 2D based emulator's.