Well, as you said... glxgears is really no indication of anything.
For example, back at my redhat 9 box, I had only mesa GL and my glxgears gave me like 4k to 6k fps. After installing fglrx, glxgears hovered somewhere in the 700+ fps. But, unlike mesa, I could run quake 3 at a stable 60-70 fps.
So, if anything... I don't think the drop of fps is as alarming as you think. I don't know why the frame rate drops though. Perhaps because glxgears is optimized to use Mesa GL, instead of Open GL.