I don't know what was updated in the last Ubuntu update--maybe OpenGL or the X server--but after rebooting my Unity desktop comes up with a blank, gray screen. Clicking on a menu item makes the screen flash for a second. A Gnome Shell environment will boot, but there are display issues: clicking on some items in the dock turns the screen blue. Gnome Classic won't boot, but Gnome Classic without effects will show properly.
I had the same problem...disabled 3D, reinstalled parallels tools...still same problem. Reinstalled parallels tools a 2nd time and now all is working, even with 3D enabled again.
Thanks for this! Rebooting without 3D and reinstalling Parallels Tools worked for me on the first try. This was driving me insane.