Does the Kindle Keyboard even support Cloud Collections? On the upside, I believe there are various tools available for managing collections on that and given firmware hasn't been updated in ages, likely guaranteed jailbreakable.
What you're describing is normal (at least on PW3 with cloud collections). It's kinda like covers - takes a while to populate. Not much you can do except wait. That is unless you want to go through the effort of manually adding the books to the collection again on the Kindle.
Note, the 999 is books inside a collection.