I had the same issue until I read that the new kernel loads modules using the major-minor numbers (not like old 2.4 kernel). So, the /etc/modprobe.conf needs to have alias char-major-195* nvidia as it's entry (NOTE the "*"). The nvidia module loads properly everytime now.
As a side comment - had the same issue with my usb module loading but the wildcard didn't seem to work so I punted and just put it in my rc.local file. (/sbin/modprobe ohci-hcd )
On the reboot, the nvidia kernel driver module is there, just not autoloading. Drivers are not deinstalled by Linux without your permission ;-)
Hope this helps.