I remember reading that this may be caused by overloading the computer's USB bus (not enough power to go around). If you have not already, try doing the following.
Shut down computer. Disconnect ALL USB devices, including keyboard, mouse, and any USB hub. Use this procedure to reset iPod shuffle
Start up computer, with nothing connected to USB, except for standard keyboard and mouse. Run iTunes. Connect shuffle to a direct USB port on computer. Attempt to sync.
If it works now, it's possible that the shuffle was not getting enough power when other USB devices were connected. Or, if it was connected to a hub, the hub was not supplying enough power. Or there may have been some othe type of USB device conflict. I would add your other USB peripherals back, one at a time, to see if the problem comes back.