I had the same problem.
I purchased Parallels Desktop for Mac Pro edition one week ago. I have a Windows 10 Pro 64-bit .iso loaded in a single virtual machine. I am not using Boot Camp. Until today, I was able to enter and exit Coherence mode with no problem; while in Coherence mode all Windows panes appeared normally and while out of Coherence mode all Windows applications appeared in the Windows 10 frame normally. I also have DuetDisplay installed on my Mac and my iPad, and have been able to use both Coherence and normal mode on both displays when shared through Duet with no issues whatsoever. I enjoy Coherence so much that I set it to my default view mode, and have had no problems at all with it since installed... until today.
Today, when I entered Coherence mode, I noticed that the taskbar was a solid grey bar, and any Windows applications that I opened were solid grey rectangles. When I exit Coherence mode they show up fine. I am running macOS Sierra 10.12.4. My hardware is a late 2016 MacBook Pro 13-inch. I have reinstalled Parallels Tools. I do not see any of the PCI Express drivers listed in my System devices in Windows. Restarting the VM has no effect. Changing the resolution in the VM has no effect. Changing the resolution in the Control Center has no effect. Restarting the MacBook has no effect. The forums do not appear to have a lot of content on this topic.
Finally I stumbled upon the Graphics menu in my Windows 10 Settings, accessed from Control Center while the VM was turned off. I increased the memory allocation from the default (512MB) to 1024MB, and lo! My Coherence mode is happy once again. Hope this helps anyone who has a similar issue.
Parallels team, you have a very nice product. I'm enjoying it a lot.