You may have just gotten the OTA update to firmware>=5.4.2, congratulations! Search for Cloud Collections here on MobileRead, and you will find plenty of shared agony about it.
The primary goal of CC is to sync all your collections across all devices. Unfortunately, this seems to include all the collections you have duplicted across e-ink, app, Fire and PC Kindles, as well as any you deleted and recreated, which Amazon has remembered.
You will need to delete the extra collections by hand -- they shouldn't ever come back, but deregistering doesn't help since your Cloud Collections are still there.
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