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Wrong popup window stacking (with raise-on-mouse-over disabled)
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If you configure E to not rise windows on mouse over (one of my preferred E configuration)
then popup dialogs of not-raised-apps appear below other normal windows

This for example is the right-click menu of gnome-terminal

Shouldn't the popups live on a layer higher than the normal windows?

I can see this behavior with every gtk app, but I didn't find any non-gtk app with popups on my system, so I cannot say if it is gtk related