I've been shading for a long time, and I've found that it's glitchy and buggy, and doesn't work the way that it's supposed to in Qubes.
This needs to be fixed.
One VM, I shade the window, click on the window behind that's in the same VM, and all I do is click on the content of the window I just shaded.
In linux, shading normally works fine, but it seems that the shading may not actually be transferring to the guests either.
This really needs to be resolved ASAP. It's the most annoying thing when using Linux the way it's able to be used. Well, maybe not the MOST annoying, because there are other things that I've mentioned in the past that have yet to be resolved that are annoying issues too. But they will eventually get fixed in 3.2 or even when 3.3 comes out.
This issue I would believe is an issue with the Qubes Display Driver and the integration of Qubes Tools passing the shading request to the Guest.