Troubleshooting Hidden/missing books on Kindle Paperwhite

[EvanRules]

Normally, books not assigned to collections appear below the collections on the home screen in collections view. My problem is some of my unassigned books are not appearing there.

I can find the hidden books by using the search feature, so i know they indeed are on the kindle. Then if I use the "add to collection" command to see what collections one of the books is assigned to, I see it's not assigned to any.

For example, I just added 9 books, and only 3 of them are visible on the home screen below the collections.

I'm using Calibre to add books. Calibre also shows the books as "on device".

This problem was happening before and after I updated to Version 5.3.6.

Any ideas how to fix this?