I found out that it happens for me after I plug in external monitor. I have to reboot the machine to get it back to normal. But the "un-minimize window" workaround works. You can argue that it is hardware related, but this does not happen with any other software that I use, including old Windows XP applications, so I think that the issue is with PL/SQL developer.

PL/SQL Developer seems to be very flaky with the latest releases. I have another complaint that they are not looking into.