jscalibrator has been known to cause problems with gamepads in ubuntu for quite some time. Did you even try to see if the gamepad worked out of the box before you installed jscalibrator? From my understanding of it, the process is as follows:
(1). Controller may/may not work just fine in Ubuntu, but for some reason users install jscalibrator anyways.
(2). Once jscalibrator is installed, it reports all buttons/joysticks/dpads working correctly.
(3a). Gamepads that worked just fine before installing jscalibrator, now experience non-responsive dpads/joysticks.
(3b). Gamepads that didn't work properly, still don't work properly with non-responsive dpads/joysticks.
Some more info:
http://ubuntuforums.org/showthread.php?t=729049
EDIT: Try and see if the gamepad works in pSX/ZSNES?