This is going to sound crazy, but at my program the rank list basically comes down to a popularity contest. In a way everyone is "equal" when they come to interview, but what differentiates people is all sorts of what I think is nonsense. The biggest question is simply personality. Do the applicants seem personable and do the faculty "like" them?
I'm at a very academic program with several MD/PhDs, a serious research program, and Holman pathway supported. Every year I see numerous high power MD/PhDs come through to interview, some who away rotated here, and they get ranked poorly because they just weren't super outgoing. It wasn't that they were bad people or pissed someone off. It was more that the faculty liked some bubbly person much more who wasn't even as qualified. Lower step score? Less research? No problem! They seemed so nice!
The other problem the MD/PhDs run into is that they are seriously trying to evaluate the program. They ask hard, serious questions about research opportunities, research time, etc... The faculty often misinterpret that as they're going to be difficult on service or difficult personalities. Some faculty do see the potential in serious residents driving the research and the field forward, but most PDs are MDs, just like our PD. Most of the faculty here and out there are MD only. They care that they'll have a resident who will run their service with the least amount of hassle possible. They want someone who will learn on their own, work on their own, not complain about anything, and always be at their beck and call--not be trying to run to a lab or a conference. It's very selfish, but it's very prevalent.
The bubbly applicants come and ask softball questions and schmooze their interviewers. I'm amazed at how easily the faculty fall for it! Some of the people I know who are very serious about coming here get ranked fairly low, while some others have little interest in the program except as a backup and get ranked highly! It's all congeniality and salesmanship.
So last year, just like this year, we're ranking all the bubbly people very highly. Meanwhile the most serious, studious applicants are ranked in the middle or at the bottom. Some well qualified applicants last year weren't even ranked because their personalities were just too flat, though I thought they were more social than some of the faculty here. I think the program just shoots itself in the foot, because some of the residents end up being very 9-5 oriented, not really interested in learning or doing research, and most interested in taking as much from the program as they can before going to private practice. But they continue to be schmoozers, and so they get by.