Something is 'Fishy' with New York's school grading system

What rule of thumb does New York use to grade it's schools? According to a New York Times report:

More than half the elementary and middle schools that got an F under the city’s new grading system are in good standing under the federal law, while more than 20 percent of the schools that the city gave A’s are considered failing, the state said.

Of the 568 elementary and middle schools that received an A or a B from the city, 398 are in good standing under the federal standards. At the other end of the spectrum, of the 115 schools that received a D or an F, 66 are in good standing, while 49 are not. Two schools that the city announced it would close at the end of this year for poor performance, among other factors — P.S. 79 in the Bronx and P.S. 183 in Brooklyn — are considered in good standing under the federal law.

There is something fishy here that we are not seeing. Perhaps this grading flaw has something to do with the "perceived character" of the students. This needs to be further investigated.