More to the point, how do I get shot of two of them?
Get a Karma.
Actually, now I think about this a bit more, Karma did sometimes suffer from similar problems if you used a Karma firmware version that didn't match your Rio Music Manager version. (This is because the collation was done by Rio Music Manager, and searching by the firmware -- if we changed the algorithm, and a user only updated one of the two, disagreements could arise.)
So maybe you should make sure your Ipod firmware and your Itunes are both up-to-date?
Peter