All files in /usr/X11R6/lib have been moved to /usr/lib since the xorg-x11-6.8.0-r4 release. nvidia-glx files should be moved as well. You have to manually copy the files to /usr/lib/modules otherwise to get glx working.
Use: openg-update nvidia emerge >=x11-base/opengl-update-2.0_pre4
That won't change anything. X complains about a missing module: (EE) Failed to load module "nvidia" (Module doesn't exist,0) (EE) No drivers avaiable That's because the driver nvidia_drv.o is still in /usr/X11R6/lib/modules/drivers. It should be in /usr/lib/modules/drivers. Maybe this is an amd64 bug since only a symlink /usr/X11R6/lib64 -> ../lib64 is created. There should be /usr/X11R6/lib -> ../lib too, am i wrong ?
Fixed in cvs for media-video/nvidia-glx-1.0.6629-r1 You were right, sorry :)
closing.