The article is not well written, and as such, it's difficult to determine for certain what data are used for the analysis. My interpretation is that they are judging schools based upon rate of improvement:

"It takes two consecutive years of adequate improvement on the MCAS to return to good standing."

I'm not sure that's a very meaningful metric. What if a school is already very high achieving? Can it really expect to make "adequate improvement," whatever that means? The article itself points out that Massachusetts is one of the highest rate states for education. Could it be that we have reached a point at which incremental improvement is going to be on a much flatter curve, and that we should not have reason to expect a sharper increase?