depending on your board type/revision it may have a few similarly looking connectors that it can plug into. be sure to read the silkscreening and i'm sure you will find the one that says "gun1" gun2 or "trackball1" and so on.
be sure you are plugging into "trackball1"
also, that input could be fried. the chip that reads the input is highly susceptible to ESD. it will need to be replaced.