Can you try resetting the devices in MC and then let MC detect your iPod. After this do the test that I mentioned earlier. Then, go to the registry under CurrentUser\Software\JRiver\Media Center 11\Portable Devices\Detected Devices and you should see one item listed. If you open it, you should see a 'Last Sync Timestamp'. Take note of that value. Then, in the registry go to CurrentUser\Software\JRiver\Media Center 11\Properties and see if you have a setting for 'Handheld - Sync Last Time'. If you do, take note of it.
Complete the test and see what results you get.
Thanks,
Steve