The Harris poll showed that the other 6 points ND could have earned (for the perfect 2875) went to Alabama, who received 6 first place votes. If I understand the scoring, Notre Dame had to receive 6 2nd place votes to get to 2869.
In the USA Today poll, ND received 56 of 59 first place votes but again fell 6 points short of a perfect 1475, which (correct me if I'm wrong) means the other three votes have to average out to third place votes. (That could mean three 3rds, or a 2nd, 3rd and 4th, or two 2nd and one 5th - some of those scenarios seem more likely than others.) Two of the remaining first place votes went to Alabama and one went to Georgia. So...Southern bias and all that, I'm sure.
Not that this is going to make Virginia Tech fans feel any better, but I think it has become obvious now that the gap in talent and/or coaching between FBS teams and the top FCS teams (not the entire division) isn't as great as we like to assume.