I am not an expert on graphics by any means, but it is logical. Visual effects of the Compiz variety (compositing effects) use the graphics card, even when they are not actively doing something fancy, because Compiz is still the one managing the screen with your game in it.

Metacity is likely not optimized for single screen, undecorated games either, but it relies on the CPU for rendering, not the GPU…

One of these days, I intend to sit down with a blank Xorg in Arch, before I put a WM on it, and try a game at full screen with frame rates counted. I bet it will have another small improvement. That’s how I use Hulu desktop and xbmc/boxee.