Alli, I'm not sure but I think I may have the same problem - not computer savvy enough to follow everything you did. But this is what I did:
1. Organised my ebooks within my Kindle Documents folder into various subfolders
2. Then took advantage of right mouse clicking on each folder to 'Create Collection from Folder'
3. Made a stack of collections
4. Renamed those collections I wished to appear first on the home list by adding a * in front of their names e.g. *Gothic
5. Comitted changes to Kindle
6. Hit eject and close
7. Unplugged Kindle from PC
8. Did a hard restart
I'm seriously bummed because although the Collections names now appear on my Kindle, many (not all) are empty - even though when I then run KCM it shows the books being in the collections. I can't determine any reason why some seem to have been successful and some have not

Can you make too many collections at a time? I made about 30 collections, with a couple hundred books, then let the Kindle alone until all re-indexing had finished.
A second issue is that the collections that I renamed with the * prefix (in order to force listing of collections on my Kindle) hasn't worked. They just appear in alphabetical order.
So where have I gone wrong? I don't understand computer speak (that's prob where I've gone wrong

just want to organise my books into less that a bajillion pages.
Adrian, if you ware out there in cyberspace - thank you so much for developing this software, it's so needed! Now this gumbee just needs a hand figuring out how to work it.
Alli - based on your previous post... do I need to go back into my Kindle Docs folder and take everything OUT of the subfolder & just have them back in a good old long list for my approach to work? Not sure if that's what your last post meant.
Thanks to anyone out there who can shed some light on this...
H