(FORTUNE Magazine) – Within a matter of 48 hours in late February, Federal Reserve chairman Alan Greenspan managed to roil the mortgage markets, gouge the stocks of the nation's two largest mortgage companies, tick off much of Congress, and send ripples of fear through millions of Americans nearing retirement. Which is quite something, since during the nearly 16 years that Alan Greenspan has been Fed chief, he has generally avoided ultimatums, doomsday scenarios, and unequivocal talk. Now, suddenly, it seems he's all about systemic risk and urgency.

Specifically, Greenspan was speaking about the risk posed by mortgage giants Fannie Mae and Freddie Mac, as well as the underfunding of Social Security and Medicare. Here's the recap. On Tuesday, Feb. 24, Greenspan testifies before the Senate Banking Committee that to minimize the perils presented by Fannie and Freddie, "preventive actions are required sooner rather than later." Then, speaking on Wednesday, Feb. 25, before the House Budget Committee, Greenspan talks about the growing federal budget deficit and how baby-boomers will soon begin tapping into Social Security. Addressing the issue is inevitable, he says, and "that action is better taken as soon as possible." No need to translate the Green-speak this time. For him that is positively pounding the table!

So what gives with Greenspan? Is the situation with Fannie, Freddie, and Social Security so serious? Is he bowing to political pressure? Or maybe Alan is going through an old-life crisis?

Neither issue is new by any means. Greenspan has expressed concern about the growth of Fannie and Freddie for years now, and so have others, especially the Wall Street Journal's editorial page. Here's the thing. Fannie and Freddie--quasi-government institutions known as GSEs (government-sponsored entities)--were created to facilitate mortgage lending to moderate-and lower-income Americans. They did so superbly. However, acting as a middleman wasn't the most profitable business. A much more lucrative business has been to borrow money from the Treasury and then purchase the very mortgage-backed securities they created. That model has worked like a charm. But it has also had the effect of ballooning Fannie and Freddie so that they now have some $1.7 trillion of debt (yes, trillion with a T) on their balance sheets.

The neocon crowd complains that Fannie and Freddie subsidize the poor--a free-market no-no. They also maintain that financial markets have evolved to the point that the interest rates Fannie and Freddie charge are barely any lower than what could be obtained through the private sector. (Those two points seem to contradict each other, don't they?) But Greenspan has focused his attention on the bigness of GSEs. He notes that the markets consider the acronym twins too big to fail--meaning Washington would be forced to bail them out. If the two did go splat (and I haven't even mentioned their gigantic derivatives positions), the fallout would make Long-Term Capital look like a Sunday picnic.

As for Social Security and Medicare, Greenspan was merely reminding us that in 2008 the first baby-boomers will turn 62, the minimum age that Social Security benefits can be claimed. In 2011 the group will be eligible for Medicare. "This is all coming sooner than most people think," says Goldman Sachs chief U.S. economist Bill Dudley.

Notes one Wall Street source familiar with the workings of the Treasury: "Greenspan knows he has a soapbox because of the election. Also he is giving these issues a little more prominence now because there is a little more urgency." My take is that Greenspan is speaking his mind without political motivation. In the case of the GSEs, I think he is right on target. But to me it's a tough sell to say that the deficit is so dire that Social Security and Medicare should be trimmed while at the same time arguing that big tax cuts should be permanent. He's walking dangerously close to the line where economics becomes politics.