For each new kernel version - or, more specifically, for each new kernel directory inside /lib/modules that you boot from - you'll need to manually recompile the driver for that specific kernel.
Originally Posted by VastOne
Did you use make-kpkg to build the kernels? If so, ensure the headers are installed, and the symlink:
Points to the location of the kernel headers.
ls -l /lib/modules/`uname -r`/build
Then manually compile the NViDIA drivers using the same method as in the guide, and then run:
that's it. No need to re-setup xorg.conf, unless you've changed back to vesa drivers.
sudo /etc/init.d/gdm start