Sorry, I couldn't find an edit button on my last post.
Anyway, I searched around some more and found this
post which I think solved my problem.
I've tested it out by deleting most of my books on Kindle but leaving a couple or so outside-of-collection books I knew were there before the problem occurred. Now when Collections is applied, all the collections followed by the books not in a collection are all showing up.
It appears one (or as I suspect, several) of the books I loaded is the culprit.
Anyway, thank you all for the replies.
