I'm assuming it's a conventional "mouse" controller. What about all its other functions: cursor control, left-click, roller if present, combination clicks? I'm also assuming you checked the cord, and that you rebooted again.
Take a look in Control Panel under Mouse, I'm sure there's a category for that whatever it's called, and you should see settings for acceleration, double-click response, perhaps button assignment, etc. Look over all options and see if something needs to be checked or whatever.
You could also try simply changing the settings, applying the changes, and then just changing them back - that would reset the controller's entries in the...Registry...shudder...