The shuffle may be losing its data connection to the computer during the time it is syncing. If you have not already, you should shut down (power off) the computer. Disconnect all USB devices (except for standard keyboard and mouse if normally used), including hubs. Do this to Reset the shuffle
Start up the computer, run iTunes, and connect the shuffle to a direct USB port. Try repeating the action that is causing the error.
If that does not help, select the shuffle in iTunes and go to its Settings screen. There is a checkbox for Enable disk use. If that setting is checked, uncheck it. If it is not checked, check it. Basically, reverse the current setting. Apply the change. See of that makes any difference.
Since the shuffle appears in iTunes, it seems to be connecting, at least initially. When you try to load the shuffle with songs manually (not with Autofill), and drag just one song to the shuffle, does it work?
As a test, try the following. On the shuffle's Settings screen in iTunes, set it to Enable disk use and Apply the change. This should make it appear in Windows. Use Windows Explorer to copy something fairly large, such as a video file, to the shuffle's disk. Keep copying files to the shuffle, until it is nearly full. Does that work without errors? NOTE: After you do this, make sure you delete those files from the shuffle (and empty the Trash).
If there is a problem copying files to the shuffle outside of iTunes, there may be a hardware problem on the shuffle. It could also be a faulty USB cable, or a problem related to the USB port.