TXgary,
I'm not sure why this is happening. If you're comfortable working with the registry you can take a look at...
HKEY_CURRENT_USER\Software\JRiver\Media Center 11\Portable Devices\Detected Devices
We use something called a canonical name to identify devices. Let us know how many entries there are for your Nano's. Ideally there will be one entry for each Nano. If there is only one entry that will explain why the syncing assignments are getting lost and if there are several entries that could explain why it's treating the device like a new device. Make sure before you check the registry that you have connected both Nano's and the Xtra (one at a time or all at the same time) while in MC so that it can generate the registry entries.
NOTE:
Make sure when you connect another device you aren't selecting "Redetect All Devices..." that will erase all saved device information and treat devices as though it's never seen them before.
Regards,
Rick