Glide64 glitch

I am currently using Glide64 0.4, and a real Voodoo3 card. The drivers are "One 3dfx Voodoo3 2.2"

What is happening is that unless I set the desktop resolution to the same as the fullscreen resolution, the FPS counter in Project64 will poke through.

I upgraded my drivers and I am using Glide64 0.41, but the problem persists. In case you didn't notice, I am using Project64.