The installer needs to see the same version of the kernel sources as the running kernel.
Make sure the "linux" link in /usr/src points to the right kernel sources.
If the installer keeps saying "Unable to determine NVIDIA kernel module filename" error after that, run it with " --add-this-kernel" option. It will create a NVIDIA-xxxxx-custom installer in the dir you have run it from. Run this custom intsaller and it all should work great..:)