Basically, here's what I discovered: they don't stick to their professed ranking system very well.
What's the problem? It has to do with the reputation score.
First, I computed all of the scores (assuming normality, etc.) and used their professed weights. After ranking them, I found the errors in the rankings (which ones were too low, too high). Then I did the same thing, except I took out the weights given to reputation score (all numbers you can verify on the internet, basically) and ranked them.
Correlation between the professed weight system and the real rankings: 0.905
Correlation between the professed weight system and the one that doesn't have any reputation score: 0.977
It is not a stretch to believe that the inclusion of 'reputation' is used to help place certain schools in more favorable places. But which get screwed when others get helped?
Schools that should be ranked 10+ places higher (i.e. the ones that got screwed or the ones where there's 'value' to be found, though they would have to be 11th or worse to begin with, list ordered from most screwed to least screwed): Oklahoma State University, Tulane, William and Mary, Missouri, Utah, Clemson, DePaul, Rutgers, Oklahoma, BYU, Brigham Young University, Wake Forest, Oregon, Iowa State, Texas-Dallas, Miami (FL), Iowa, SUNY-Albany, UConn.
Schools that should be ranked 10 or more places lower (i.e. they were helped out - they have to be ranked 72 or higher to begin with, this list is order from least to most help): University of Michigan, UNC, Vanderbilt, CUNY, Purdue, Boston, Michigan State, GA Tech, Wisconsin, CWRU, GWU, Colorado, Georgetown, Boston College, Washington (St. Louis), Penn State, UC-Irvine, TAMU, SMU, Indiana, Rochester.
Law schools will be forthcoming.