ah, I see better what's happening. Putting translateZ(0) on the #site makes #site act "a containing block for fixed positioned descendants." (http://www.w3.org/TR/css3-transforms/#transform-property). This means that fixed-position elements inside of #site no longer are positioned relative to the viewport, but instead relative to the #site element.
@minrk - I've been playing with the translateZ(0) on #site being turned on and off, and looking at the paint rectangles in Chrome 40 and Firefox 33, and I don't see any difference in the repaints with having the translateZ(0) on or off.