The attached patch will prevent showing notifications when a window on the screen is in fullscreen-mode. It's not perfect, it's just skips displaying the notification instead of postponing it.
Created attachment 3325 [details] [review] use wnck and don't show notifications if another window is fullscreen The size-checking (workaround comment) is for the bug: http://bugzilla.gnome.org/show_bug.cgi?id=316700 in libwnck that is already fixed in cvs. So it's probably save to remove it and just use is_fullscreen(win) without additional checks.
Michael Vogt, Do you still experience this issue with newer soft? Please check the status of your issue.
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