SOLVED IT!!
Ok this makes no sense to me whatsoever, but since it was working in the MOBI format I concluded that it was not my database or id's or anything like that and since I determined that it was also not any of my metadata templates, the only thing left that I could see left to try was the AZW3 output options.
I unchecked the option for "Enable sharing of book content via Facebook, etc WARNING: Disables last read Syncing"
reconverted to AZW3 --->send books to device ---> create collections from kindle collections ---> import collections from calibre via CM
Voila, success, collections now auto-populate with books in AZW3
No clue as to how or why this fixed it but it did.
Chrysandra
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