performance problems solved by resizing window


I have a problem with my application. It runs with a good framerate about 50 to 120 fps in any resolution up to 1024 because it is CPU Bound on my computer.
But after starting it sometimes performance drops to 1 fps or lower like it would do software-rendering. But if i make the window smaller the framerate goes back to normal. And it stays on that level when i make the window larger again, even larger then on startup.
The only thing i do during resize is changing the Viewport and adjusting the projection matrix.
Whats causing this?
Its done on a GeForce FX5800 with 45.20 drivers. The card has 128 MB RAM and the app only consumes about 10 MB for texture memory, And the geometry is below 20000 Polys per Frame. So there should be no memory problems.