It seems clear that CC is not seeing the same library that calibre is seeing. Why is a mystery.
First question: is there a reason you haven't updated CC? There have been two releases after 5.1.2.
Second question: are you sure you CC is using the same cloud account as the machine running calibre?
Third question: is there something on the computer that runs calibre that is updating the Amazon cloud account? Some background app? If not, your changes will be local but not show up in the cloud. You can check this by going to the cloud account and verifying the dates on calibre's metadata.db, and checking if the new book folders are there.
As far as I can tell, the official Amazon Cloud Drive app does not do background syncs. At least my copy doesn't. In fact, it doesn't seem to overwrite changed files when doing a manual upload, which makes it worse than useless.
If you send me a CC debug file I can verify what folder CC in Amazon's cloud that CC is checking and the last modification date of the calibre database. See our FAQ
How do I get help? for instructions. Please erase the multipie.co.uk To: address.