Curiously I have a similar issue. I get fairly slow framecount unless I log in as root. Then I get about 20 times the number of frames per second. Any suggestions/similarities?
I wanted to check FlightGear, therefore I had to activate 3D and accel. I downloaded the newest nvidia driver, NVIDIA-Linux-x86-1.0-8776-pkg1.run. I modified /etc/X11/xorg.conf in the same way I had done previously in 9.3 where it worked, and rebooted.
I try "glxgears", small window:
cer@nimrodel:~> glxgears 3596 frames in 5.0 seconds = 719.072 FPS 4023 frames in 5.0 seconds = 804.191 FPS 4011 frames in 5.0 seconds = 802.194 FPS
full screen
697 frames in 5.0 seconds = 139.220 FPS 652 frames in 5.0 seconds = 130.221 FPS
The gears turn slowly, and the main cpu soars to 100%. This is not normal.
-- JDL