Oh, how we all are affected so easily by a for-profit magazine. I really wish there was a competing, credible, unbiased, and alternate source for med school rankings. Maybe the NYT, Guinness Book of World Records, or some other body could put out their rankings. Then we would have two sources to use and to compare and to rack our brains over.
The two schools are vastly different, are they not? Does MSSM have PBL? They have really different curriculums, different locations, different student bodies (I'm sure you know about that because you interviewed at both places).
I appreciate that your decision is hard, but I don't think there are too many similarities between the schools. So you gotta make your feature priority list and decide what's most important to you. Which place will make you more happy on a day-to-day basis.