What you see above are all hidden windows. But the BTT windows aren't hidden—they aren't even open or even existing. At least, I'm not aware of them. Even the BTT configuration window is closed. Is this a bug?
can you check whether 6.314 resolves this on your macOS version? (uploading now)
Thanks, Andreas. I'll have to test this for a few days because I don't know how to intentionally display those ghost windows.
Edit: But I've already noticed something: The behavior of the window/menu has changed in such a way that not all apps regain focus when the menu is closed without selecting a window. Unfortunately, that's a drawback.
If you want to test, try with TextEdit.

