We had a problem with our PPC campaign recently. Even though we had unoptimised the ad delivery we noticed one ad getting more traffic than the other. Now this did not seem like what should happen so we contacted Google thinking maybe we had found a bug in the delivery system.
In actuality we had found an impacting variable that is not generally known. Quality scoring impacts the delivery of your ads - one can get a better score and that will influence delivery even when asking for even flighting.
Obviously the QS impacts the real CTR - but behind the covers.
A rep at Google explained it this way:
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!
Figured I would pass this along for comments. I have opened a forum thread here.