Same problem here. Window border colors are no longer working since today's update on Qubes 3.2-rc1. How can one restore it back to its original working state? Since this update every time a command is launched, when the respective AppVM is down, the window is not displayed and the AppVm shows as being in a transient state (for instance, when launching the gnome-terminal, the terminal console only gets displayed after another instance of gnome-terminal is launched, then two terminal console windows are displayed) Something definitively went wrong with this update...
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