I've noticed some ATI cards flip textures some times too... not sure why.
It could be that some matrix is getting a negative sign somehow... or some other random reason. Perhaps something to do with the perspective matrix.
Are you using glReadPixels? I've heard that sometimes flips things on different cards...
Any idea what could possibly be causing these problems? Is there some function that flips the framebuffer's texture? What am I missing and what's going on?