Thank you for sharing when this happened - it's happening to me now, over a year later. I called one of our vendors because the checks were showing on the uncleared check report from a month ago and she said they'd already deposited it. When I clicked into the check from the report, it showed a link to the bank match in the upper left corner. It should have been marked as cleared when I matched it, but for some reason it wasn't. 

I immediately searched and found your post and followed the advice to manually clear it from the bank register. This is tedious and unnecessary, but at least there's a solution to keep the books in order. I'm hoping that the bug will be miraculously fixed for me in a couple days too