I can attest to still being afflicted by this bug. Pretty annoying, but at least it doesn't break my games as long as I hit F6 a few times after capping a city. Other popups tend to accumulate though. Verifying the game cache doesn't actually fix it for me either, which is a little surprising because I would have assumed it includes checksums for game files. I heard it was bug with an improper close trigger(s) in the lua for the tech tree screen.