I use Parallels Desktop 12 for Mac Pro version 12.1.3 and my support code is 78950-21405. On occasion I've noticed that when Parallels is running, that when minimizing either an OS X or Windows app, the app doesn't minimize into the application icon but rather I get a little picture of the minimized app at the right side of my dock. Note that my Apple "Minimize windows into application icon" option is checked and unchecking and rechecking doesn't help. In order to restore that functionality I have to reboot the Mac.
Hi Martin. So the issue doesn't start as soon as you start Parallels, but rather randomly while running Parallels, is that right?
Ok, let's try this: The next time the issue occurs, do not restart your Mac. Please shut down Windows (as opposed to simply leaving it in suspended state; see http://kb.parallels.com/123111 for details) and quit Parallels Desktop completely. Check if the concerned functionality returns as soon as Parallels is quit.
I thought of that and it didn't work. BTW I contacted Apple support yesterday and they couldn't find anything wrong with the way OS X was working. They did however have me do a PRAM (Command + Option + P + R) reboot and since then the problem hasn't happened, but it's been less than one full day. If it happens again I'll post again.