Secondary mortgage market investors may be a bit “too euphoric” following this week’s settlement between Bank of America (BAC) and Fannie Mae and Freddie Mac, according to one policy research firm. MF Global said it’s still hard to gauge the real price of the repurchases by the bank, the deal only covers conforming whole loans, and the larger private-label mortgage-backed securities fight still looms. Analysts at the Washington think tank said there now is also additional pressure on other banks to settle with the government-sponsored enterprises. Shares of BofA closed Monday up 85 cents, or 6.4%, to $14.19. The stock was off a nickel to $14.14 in trading on the New York Stock Exchange early Tuesday afternoon. Bank of America agreed to pay nearly $3 billion to Fannie and Freddie, which equates to 39 cents on the dollar or about 20% less than the 50 cents on the dollar the Congressional Oversight Panel recently estimated. “Yet that does not mean Bank of America got a bargain,” MF Global said. “The bank has been paying out on GSE loans for many quarters. The first loans that the enterprises returned contained the most obvious defects and defaulted quickly. That means the most recent put backs – those covered by the settlement – may be less clear cut.” The bigger, private-label fight for banks may very well become even more important to BofA. MF Global said the danger lies in the possibility the Federal Housing Finance Agency will continue to see if the bank still owes the GSEs money, if BofA doesn’t settle with institutional investors as it did with the GSEs and Ally Financial last week. The firm said the FHFA could use its regulatory powers to gain access to files the private investors would have trouble obtaining. “We remind investors that one investor group alone is seeking $47 billion in put back claims against Bank of America,” MF Global said. Also additional settlements between the GSEs and smaller banks “could also lead to pressure on Bank of America or other lenders to settle private-label MBS claims at a higher price than may be warranted had there been a more comprehensive review of the claims.” Earlier Tuesday, Keefe, Bruyette & Woods said it revisited its representations and warranties estimates for the mortgage industry on loans originated specifically to be sold to the GSEs following the settlement with BofA and Ally. Author holds no relevant investments. Write to Jason Philyaw.