Windows 10 and virtual desktops
It does not do it always.
Before Windows 10, I would get this sometimes with VirtuaWin, but not nearly so often and flicking back and forth between desktops, or changing which Window had focus before switching was a work around. This does not seem to work with Windows 10's virtual desktops.
I can't get it do this right now, but I think if you don't use the hotkey to switch desktops, it does not trigger the issue.
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