I have an interesting situation that may or may not be related to what's happening with the previous poster.
I updated to the most recent version of the plugin. This was the first chance I've had to take the GUI for a spin (and it's SWEET!). I backed up my collections, fired up calibre and looked it over. I realized that the simplest way to preserve the collection my games were in was to take out any calibre managed content and remove that tag from calibre so it would be a "Kindle only" collection.
So, I made the changes. As a result, I no longer had an "Active Content" tag in calibre, hence, no more "Active Content" collection managed by calibre, right? Wrong. Even though I pushed the new metadata by removing and re-adding a book to the Kindle (and checking the timestamp), the plugin overwrote the collection on the Kindle, kicking out my games. I thought, okay, maybe I need to get tough with it, so I moved my games to a "Games" collection, then deleted the "Active Content" collection and moved the remainder files in with the games for the sake of the exercise (the other two files were my clippings.txt and that Books of the Web thing. Note: BOTH of these items had not only been untagged in calibre, they were DELETED from calibre and existed only on the device.
For extra measure, I ejected the Kindle, restarted calibre and reconnected the Kindle, checked to make sure the new metadata file was pushed (it was, time stamp was that minute), ran a "preview" with the plugin. Same results. An "Active Content" collection was (re)created, and those two files were put in it, even though they were no longer even in my calibre library.
Somehow, somewhere, the metadata isn't getting fully updated or something. Even after much fiddling (including putting three new books into calibre and transferring those to the Kindle) it still thinks that I have those two files in calibre and the metadata that was attached to them. I finally gave up and simply deleted the (now redundant) collection from the Kindle.
Every other thing is 100% correct. New books added went into the correct collections, my other Kindle-only collections were untouched. I didn't save the text file, unfortunately, but I will try to recreate it tomorrow, though I don't think it will show anything that I haven't already covered.
The reason I think it could be related to the previous poster is because of the extra tags - they may no longer be in their library because they cleaned them up after import, but it seems possible they may be in the metadata file getting pushed to the Kindle since I've got at least one tag and two files that won't surrender and die.
This is seemingly an issue with that metadata file, not the plugin, and tomorrow if I don't have a headache I will crack open that file and look for the culprits. Perhaps a little library maintenance will fix the problem. I will report back with the results, as it may help someone else who has "mystery collections" popping up.