Comment 39 for bug 687567

You can see similar "flashes" in some apps if you have a fade-out effect set for closing windows. Closing Thunderbird you see the same kind of white flash as this bug discusses. Closing Chrome you see the client/page area similarly flash to black while the window fades out.

At a guess, it looks like the "flashing" is the result of windows, or sub-windows, being explicitly unmapped by the application before they're destroyed. So I doubt this is actually a bug in the compiz effects, but the apps themselves, including the code that renders indicator menus, need to be made to not unmap their windows if they're being destroyed anyway. That might stop this problem from occurring. Just a theory.