The Associated Press is reporting that one of the big three credit-rating agencies, Standard & Poors, has agreed to pay $1.38 billion to settle with the U.S. government, 19 states and the District of Columbia. This S&P settlement is purportedly to atone for its role in the 2008 financial crisis, when S&P and the other ratings agencies — Moody’s Investors Service and Fitch Ratings — gave various mortgage-backed securities their highest ratings. But there are complexities to this story that have gone largely unreported.

True, S&P’s top ratings did give signals to investors that the securities were safe when, as it turned out, they weren’t. As a result, trillions of dollars in such securities were bought and sold, as investors snatched up securities that paid a surprisingly high rate of return.

The AP story notes that there seems to be a conflict of interest in the way ratings agencies are paid. Rather than being paid by investors, the agencies are all paid by the companies creating the securities. This gives them an incentive to inflate their scores, since companies who frequently get low ratings for their investment products from, say, S&P, might take their business to a more lenient ratings agency.

This is a serious problem, and it needs to be fixed. I wrote about it in detail in my 2013 book Infiltrated. Ratings agencies used to be paid by investors, but this was changed because, well, large investors didn’t like paying and they enjoyed a lot of political clout.

Unfortunately, the 2010 Dodd-Frank “Wall Street Reform and Consumer Protection Act” created all manner of  counterproductive regulations but left untouched this obviously dysfunctional arrangement between companies and their ratings agencies.

Bad scoring by ratings agencies probably did contribute to the 2008 financial crisis, but it was only a contributing factor, and far from the most significant one. If the federal government had not aggressively scrambled market incentives with its well-intended but misguided “affordable housing policies,” there would have been no crisis.

The most that we can say is that the agencies played a role and played with fire. But in my own research, I found no clear evidence of actual fraud by any of the ratings agencies. And none is being reported as part of this settlement, despite the mea culpa issued by S&P, no doubt to make the case go away.

But the more pertinent and troubling issue is this. The AP reports correctly that “the three big rating agencies — S&P, Moody’s Investors Service and Fitch Ratings — have been blamed for helping fuel the 2008 crisis by giving strong ratings to high-risk mortgage securities.” But if all three ratings agencies made the same mistake, and so contributed to the financial crisis, why did the Justice Department under Eric Holder not go after Moody’s and Fitch at the same time?

There’s only one obvious difference: Standard & Poors lowered their long-term sovereign credit rating on the United States in August 2011. The other two rating agencies did not. The US Justice Department quickly launched a probe against Standard & Poors for its alleged role in the 2008 financial crisis, and then brought suit against the agency in February 2013; but has taken a much more leisurely tack with Moody’s and Fitch. Only now, years later and with the case against S&P settled, do we learn that the Justice Department has started “probing” Moody’s.

Was S&P punished by the Justice Department for calling even slightly into question the long-term credit-worthiness of the federal government? Hard to say. If so, it may be an abuse of political power ill spent. By the time corporations and the federal government have finished pressuring and manipulating these ratings agencies into playing Pollyanna in the face of the darkest storm clouds, global markets may already have moved on, no longer interested in a system in which the rating umpires are paid and pressured by the players.

Jay Richards is the Executive Editor of The Stream and the author of Infiltrated, which describes the events and key players that caused the 2008 financial crisis.