I've been seeing the same behavior for the past 2-3 months, and I've been trying to characterize the behavior to debug it. Until I saw this forum, I thought it was only me. Here's my set up and what I've learned:
1. I have 2 Thunderbolt displays attached to a MacBook Pro (cover closed) with an 8-core Intel Core i9 with AMD Radeon Pro 5500M 8 GB and Intel UHD Graphics 630 1536 MB. I'm running MacOS Monterey 12.5.1. I'm running Windows 11 in Parallels 18 Pro Edition Version 18.1.1 (53328).
2. My dock is on the right side of the right Thunderbolt Display.
3. The gray box periodically (every 5 minutes or so) appears on the left side of the right Thunderbolt display and remains for a few seconds, as shown in in the screenshot below. It is always the same size and at the same location. Also, when Windows Defender shows a notification in the lower right hand corner, when I click it to go away, the Windows Defender notification disappears, but then I can see a gray box behind the notification that remains for a few seconds and then goes away. No gray box ever appears on the left Thunderbolt display.
4. For the few seconds before the big gray box disappears, it stacks with other Mac windows. So, I can click on it to bring it to front, or I can click on other Mac windows to bring them to front over the big gray box. So, Coherence appears to be creating a phantom Mac Window.
5. When I am running Windows 11 in Coherence, but I have no applications open, the big gray box does NOT appear. BUT, if I have any application open (I've tried several Office apps, Photoshop, Windows utilities), whether or not the application has a window visible, the big gray box periodically appears. As soon as I exit all Windows applications, the big gray box stops appearing. So, the big gray box is somehow related to a Windows application running, whether or not the application's window is visible or minimized.
6. I'm not completely certain about the following possible symptom because it happens very fast: when I am typing in a Mac Window and the big gray box appears, it seems to take away focus for a moment, messing up my typing. But it's possible that I simply get distracted and mess up the typing myself.
This a major bug and that is really disruptive. It's gotten to a point where I quit all Windows apps and relaunch them only when I need them, and then quit them again, because it is so distracting to have the big gray box appear.
Good luck tracking down the bug and fixing it.
