Problem with FBO

So I really stuck with this one.
I have some impostor shaders that convert a reactangle into a complex geometric shape. Also the application uses frame buffer object for implmementing shadows. So I render the same image once into the framebuffer and then onto the screen.
Recently I had to change the algorithm in the shaders, it uses more matrix operations now but less trigonometry functions.
Everything worked OK before it. Actually it still works fine when rendering on the screen.

However when the rendering is reditected into the frame buffer the more complex shapes SOMETIMES are not rendered.
There is no problem with newer videocards, but nVidia FX 1400 and FX 3450 render these shapes maybe 3 times out of 10 frames.

I do use glFlash ( also tried glFinish) just before switching from FBO to screen rendering but it does not help.

Is there something obvious I miss ?