Fannie Mae / Federal National Mortgage Assctn Fnni Me (OTCBB:FNMA) and Freddie Mac / Federal Home Loan Mortgage Corp (OTCBB:FMCC) may have gotten pounded last week by a federal court ruling, but both stocks are rallying strongly today. Bill Ackman’s Pershing Square Capital Management is said to have increased its stake in both firms, bringing those stakes up over 10%.

Ackman raises Fannie Mae, Freddie Mac stakes

Michelle Celarier of the New York Post reported about his increased stake, citing unnamed sources. Because Pershing no longer reports its stakes in Fannie Mae and Freddie Mac, it isn’t clear just how large the firm’s holdings in them are. The U.S. government, however, owns 80% of both of the mortgage companies.

On Sept. 29, a judge tossed out lawsuits filed by Perry Capital and Fairholme Capital. Both firms are preferred shareholders and alleged that the government took their property by changing the terms of its agreement. After that news, shares of both Fannie Mae and Freddie Back plummeted, falling as much as 50% before today’s rally.

Ackman’s case contines

Bill Ackman’s firm has filed its own lawsuit in connection with the same issue, but his case was not included in the ruling made on Sept. 29. Ackman’s case against the U.S. government was filed in the Court of Federal Claims, and according to the New York Post, investors think that is the right jurisdiction for his case. Perry Capital’s case was filed in U.S. District Court.

Fairholme Funds isn’t giving up

Also Bruce Berkowitz of Fairholme Funds has filed an appeal on its case against Fannie Mae and Freddie Mac.

In a statement, Berkowitz reportedly said that they are “confident that Congress did not authorize the conservator – a Federal agency – to operate a profitable financial institution perpetually, to strip away all of its capital, to pay all its future profits to another Federal agency, to violate the order of priorities of corporate law, to transfer its assets without determining fair price, to replace the organized claims process of receivership with the self-dealing expropriation of private property, or to make corporate governance decisions without a standard of care,” according to Forbes‘ Nathan Vardi.

Perry also said recently that it is appealing that decision.

Fannie Mae, Freddie Mac Surge, Thanks To Ackman