When you trigger GPU compositing (eg, through CSS animation), the browser sends that element to the GPU, but also anything that would appear on top of that element if its top/left properties were changed. This includes any position:relative elements that appear after the animating one.
The solution is to give the animating element position:relative and a z-index that puts it above everything else. That way you get your animation but keep the (superior IMO) sub-pixel font rendering on unrelated elements.
Here’s a demo of the problem and solution http://www.youtube.com/watch?v=9Woaz-cKPCE&hd=1
Update: Newer versions of Chrome retain sub-pixel antialiasing on GPU composited elements as long as the element has no transparency, eg has a background with no transparent or semi-transparent pixels. Note that things like border-radius introduce semi-transparent pixels.