Strange FPS problem

Hello there,

i have a strange slow down in my opengl
isometric engine.

When i render the background tiles to the
isometric viewport (Main window) and a
perspective viewport (sub viewport in main
window) i get 638 fps, however when i
render just to the isometric viewport i get
just 198 fps.This is very strange as only
half the tringles are being rendered and there is one less call to clear of the
depth buffer.

Does anyone have any ideas whats going on.

Im using an ATI Radeon 32DDR with a 1.3gh P4.

Thanks in advance.