I only have one profile loaded for the player but it see's it twice

Whoops! My bad.

Unfortunately, the sync profile is keyed by device serial number (look in HKEY_CURRENT_USER\Software\Rio\Rio Music Manager\2.0\devices\Rio Karma for the gory details). So if you've got it plugged in twice, it'll do exactly as you describe.

I don't have a workaround that I can suggest, though.

I've posted a link to this thread on the Beta test forum.