don't underestimate the importance of "non-paper" factors when it comes to the application process.
paper applications are great; they form the basis for whether or not you will get interviews. my guess is that a lot of these people with great numbers were interviewed at most of their schools (unless their essays were poor).
but once the interview starts, it is a whole different ballgame. med schools are looking for students that are not only smart, but also confident, have personality, are fun to be around, and people who will make good colleagues. They are looking for people they feel they can learn something from. Things such as maturity, mental strength, sincerity and insightfulness take on foremost importance, contrary to common belief. But the most important thing, I believe, is confidence. If some 3.95/38R student walks into that interview room and can't look the interviewer in the eye, you might as well throw those numbers out the window. Those top-echelon schools arent looking for cookie-cutter doctors who do well on tests; they are looking for people who are confident and mature enough that they will shape the future direction of medicine and be leaders in their field. These interviews are how med schools find out if you are hiding behind your numbers or if you are standing on top of them.
This may sound like a lot to ask of a person. But nevertheless, med schools ask. That is why so many great candidates apply to these top schools, and only ~5% get accepted.
There may also be many subjective variables that come into play. I've had interviews where I was told I was a great candidate and I'd probably get in. But then I don't. This seems happens to everyone for at least one school. Apparently the people on the admissions committee disagree with the interviewer. Who knows what part of your application they dissected to reach that conclusion.
So, at the risk of sounding like a preacher, don't get caught up in numbers or worrying about what admissions committees will like, as most of us do at some point. Concentrate on doing your best, being strong, being smart, and being yourself. Make them want you, instead of you wanting them. The rest should work itself out.