Comment 4 for bug 331005

That's most likely due to the notification/bubble-windows not being skipped by the window-match rules for the fade- and animation-plugins of compiz. Newer compiz package should automatically bring you these fixes.

If you prefer to use a custom compiz profile, just make sure you add

!(title=notify-osd)

to the window-match rule of any animation- or fade-plugin setting that might mess around with fades or other manipulations of windows.