AussieWebmaster has posted information in a Search Engine Watch Forums thread where a Google representative has told him that Google's quality score helps determine the ad delivery. Here is the quote:
Regarding the serving, this actually is a common question that we receive. The system tries to equally rotate ads but there are other factors that weigh into this rotation. In your case it does look fairly even for the most part, however the system may be looking at the one ad as one with a less quality score than the other, thus not serving it as often. Although you have it opted into rotate more evenly it isn't guaranteed that the system will functionally work to an exact science. I know this isn't the answer you were hoping for, but this is what we have been told by engineering!
Jonathan Mendez has a great case study blog post from a while back that goes into more detail on What Google’s Quality Score Is & What It Is Not. This post helps clarify the message above.
Forum discussion at Search Engine Watch Forums.