"It doesn't belong here or is a duplicate" flags (which are only available as long as you cannot vote to close) aren't sent to the moderator flag queue anymore, but to the close votes review queue.
Your close flags will probably be active until the associated, unhandled review entries (example) are either accepted or declined by enough reviewers. The queue right now contains over 500 questions, so it might take a while, but there are several very active reviewers, so it shouldn't stay active indefinitely.