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I don't know whether you've abandoned this magnificent piece of software or not, but here goes anyway:
In order to get around the "problem" with not being able to control "cmd.exe" windows, it would be nice with an "Always below" option for the other (VD-controllable) windows. Then, I could at least move to a desktop, and ask the "opposite" (non-cmd.exe) app. to stay at bottom - that would save my day...
What do you think?
I'm all alone here, but for the record: I just found that I can indeed make "cmd.exe" windows appear "Always on top": Just right click the "cmd.exe" in the "Dekstop preview pane" and choose it from there!
That saved the day for me!