Can't get info from Joysticks

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Here's some extra info about my problem. Here's the output from driver station:

WARNING <Code> 44008 occurred at FRC_NetworkCommunications <radioLostEvents>  0.000 <radioSeenEvents>

WARNING <Code> 44007 occurred at FRC_NetworkCommunications <secondsSinceReboot> 3.435

WARNING <Code> 44008 occurred at FRC_NetworkCommunications <radioLostEvents>  290.037 <radioSeenEvents>

WARNING <Code> 44007 occurred at FRC_NetworkCommunications <secondsSinceReboot> 292.570

Modified Network Configuration: Set 
I/O unit not detected or not installed correctly.

Here's all of the code I'm using for this test:

package edu.wpi.first.wpilibj.robottest1;


import edu.wpi.first.wpilibj.Joystick;
import edu.wpi.first.wpilibj.SimpleRobot;

public class RobotTest1 extends SimpleRobot 
{
    public void autonomous() 
    {        
        Joystick joy = new Joystick(1);

        while(isAutonomous() && !isDisabled())
        {
            System.out.println(joy.getX());
        }
    }
}

The output constantly says 0.0, whilst I'm frantically moving the joystick around... Yet this was all working fine last year. Once again, the driver station appears to identify my joystick on the setup page, as it flashes blue when I press the buttons. Windows game controller properties sees the axis movements fine.

Here's the differences I identify from last year:
- Netbeans FRC plugin updates
- Driver station update
- SmartDashboard update
- USB-splitter plugged in, but I have tried both the splitter and a direct USB connection
- New, imaged cRIO 2013
- Installed FRC Utilities and Labview package 2013

One thing I just noticed is that I believe I haven't installed an even newer driver station update from 01-05-2013. (But that may have been included in the Labview DVD install... But I'll download it anyway).

I will post back later when I get more info. Please share your thoughts, thanks.

EDIT: Ahh wait... could it be because I'm doing this in autonomous mode? Are the controller connections blocked in autonomous? I'm going to feel really stupid if that's all it was xD