Can't get info from Joysticks

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I have a rather strange problem similar to this: http://www.chiefdelphi.com/forums/sh...d.php?t=103097

So far I have tried getX() and getRawAxis(), and they all return 0, even when I'm using the joystick. I have tried two gamepads and one Joystick, which has worked previously, but currently am unable to get any input in the code. I have been updating all of our software, and I imaged our new cRIO to the latest one. I have been testing this alongside some SmartDashboard code (which seems to work fine). The strange thing is that the driver station seems to identify my controllers just fine, and it flashes blue whenever I press a button. Maybe its something I need to configure in driver station, or the Netbeans project? Has anyone else been having trouble getting input from the joysticks? I will try a few more things on our next robotics meeting, but I'd appreciate any thoughts you guys have on this. Thanks!