Re: VSYNC Frame Counter
glXQueryFrameCountNV has to read the frame count from the gsync device over a very slow data link.
glXWaitVideoSyncSGI could be getting confused by on-demand vblank interrupts. Please try disabling that option to see if it returns better numbers.
If you continue to have trouble, please contact developer relations through the NVIDIA developer program, since they'll be better equipped to help you.