Comment 12 for bug 548981

Maybe the /usr/share/update-notifier/notify-reboot-required could check the /var/lib/dpkg/lock, and keep the loop until it is clean.
Or maybe even whatever (applet?) watchs for /var/run/reboot_required should watch the dpkg lock as well and display the red only when reboot_required is present and dpkg/lock is not. So when you start a second upgrade or install, it would turn back to black.