Comment 36 for bug 106217

As I don't have nvidia hardware, I'm not likely to be able to help with any underlying problems.
I hadn't realised there was common practice for people to be installing non Ubuntu versions of these pacakges.

If there are bugs with the Ubuntu shipped verison of the drivers, please find the existing bug which matches your symptoms exactly, or open a new one. Often part of the debugging process will be to produce a "propper" .deb package of a newer driver to test, which shouldn't suffer the kind of conflicts you'll get using tools like automatix.

uptate-initramfs causing breakage may indicates that the modules you have installed have corrupted / conflicted with those already installed. update-initramfs copies various modules (including some of the agp drivers and dri modules etc..) to the ram disk where some modules load from, so you may not have been loading them before now.

update-initramfs -u should uptate due initrd corresponding to the currently running kernel. I don't know why its updating different files each time you booted.

If you're having issues still, I'd suggest using aptitude to remove and re-install the latest kernel (linux-image, linux-restricted-modules and linux-ubuntu-moduels at least).