Odd this. I've just done a disc full of Megadrive stuff, with the latest Fusion, for a mate and he's complaining of the same thing. He says it calibrates fine, but when he goes to play his fave (Streets of Rage), the characters legs move but he doesn't go anywhere! With the keyboard he says it's fine. He's only got a PC digital pad, like a SNES one, with no analogue control, but I reckon it should still work.
I myself use two different dual analogue PC pads and they're both fine in all mu emu's, so I couldn't help him out. If anyone has a solution I would be most grateful of the opportunity to pass on the wisdom to my mate.