No you are not the first one, but I do not think anyone knows what the "right" way is to clean them up. The longer you have your devices and the more you change your collections the worse it will get. I still have collections showing up during the import which I have not used in three years, not to mention devices showing up on the list that are not on my MYK page on Amazon's servers.
The only device I can tell you is pick the device that needs the most corrections, remove all the books from those collections and then delete the collections. Allow a day or two to sync them with Amazon's servers, and then import them from the other device.
Usually after I have my collections setup, I only make manual adjustments on both devices rather than continue to use the import feature.