I have a machine which requires the new AMD fglrx binary module (8.41), which Ubuntu gutsy does not include - so I've installed the AMD package and I'm managing it manually. To prevent Ubuntu from overriding the manually installed driver and replacing it with the old driver managed by the "restricted modules manager", I had to edit /etc/default/linux-restricted-modules-common and add "fglrx" to the DISABLED_MODULES line, and also edit /etc/modprobe.d/lrm-video and disable the "install fglrx" line.
When I upgrade the linux-restricted-modules-common package, the lrm-video modprobe configuration file stays as I've set it, but the /etc/default/linux-restricted-modules-common configuration file is being reset to how it was before (with nothing disabled), which causes the next reboot to have the old driver linked to the kernel and as a result the system freezes when X starts loading.
Currently I have to manually make sure that both /etc/default/linux-restricted-modules-common and /etc/modprobe.d/lrm-video have fglrx disabled after each time linux-restricted-modules-common is updated.
If you manually install upstream versions, you need to maintain them by yourself. In hardy though, envyng will take care of installing upstream versions.