My Windows 10 VM on OS X 10.11.6 was operating very well, booting speedily, all features error free. I foolishly installed the latest upgrade to Parallels 12.1.1 (41525) and my VM is now seriously damaged: (a) boot time has gone from 60 seconds to 10 minutes; (b) keyboard is not recognized in Settings, Cortana, or any Modern app; (c) Windows no longer recognizes keyboard actions from Devices > Keyboard; (c) every time I boot all pinned items in the taskbar disappear. Short of reinstalling Windows (which I will not do because I am not interested in having to reinstall and reconfigure all apps from scratch), I have booted into Safe Mode repeatedly; used DISM to RestoreHealth; created new user accounts to test if the bad behavior occurs there as well (it does).
Nothing else changed in this VM except the Parallels "upgrade".
Nothing else changed in this VM except the Parallels "upgrade".