The boxes on the Acid3 results page are 1 pixel further apart from each other when rendered by WebKit than they are on the image Hixie posted as the reference rendering.
Hyatt said that it might not be a bug, and instead may be some kind of rounding issue that's not guaranteed by any standard, but I'm not sure if that's right. Filing a bug so we can keep track of this.
A change to Acid3 itself took care of this. No action required in WebKit now.