check to see if you have 5v on the power pins of the joystick port. i think it's the center two pins of the bottom row of the db-9 connector. Later Amigas had a pico fuse in the 5v line, but the 1000 didn't. It can vaporize a mobo trace if something shorts the mouse port. The mouse buttons and joysticks will still work, cuz they're just switch closures.
