Bank of America has long rued its 2008 decision to acquire Countrywide Financial, the subprime mortgage giant. To date, the bank has set aside some $40 billion to settle claims of mortgage misconduct that occurred before it acquired the freewheeling lender.

It has been a regular refrain at Bank of America. Last month, Brian Moynihan, the bank’s chief executive, told Bloomberg television at the World Economic Forum in Davos, Switzerland, that carrying Countrywide was like climbing a mountain with “a 250-pound backpack.”

But according to new documents filed in state Supreme Court in Manhattan late on Friday, questionable practices by the bank’s loan servicing unit have continued well after the Countrywide acquisition; they paint a picture of a bank that continued to put its own interests ahead of investors as it modified troubled mortgages.

The documents were submitted by three Federal Home Loan Banks, in Boston, Chicago and Indianapolis, and Triaxx, an investment vehicle that bought mortgage securities. They contend that a proposed $8.5 billion settlement that Bank of America struck in 2011 to resolve claims over Countrywide’s mortgage abuses is far too low and shortchanges thousands of ordinary investors.

The filing raises new questions about whether a judge will approve the settlement. If it is denied, the bank would face steeper legal obligations.

Lawrence Grayson, a spokesman for Bank of America, denied the bank was putting its own interests ahead of investors.

“Modifying mortgages for homeowners in severe distress is critical to the ongoing economic recovery and is encouraged by the government at all levels,” he said. “It is difficult to see how federally regulated entities like the Federal Home Loan Banks would seek to attack that practice which helps families to stay in their homes and in no way violated the contracts at issue.”

Among the new details in the filing are those showing that Bank of America failed to buy back troubled mortgages in full once it had lowered the payments and principal on the loans – an apparent violation of its agreements with investors who bought the securities that held the mortgages.

An analysis of real estate records across the country, the filing said, showed that Bank of America had modified more than 134,000 loans in such securities with a total principal balance of $32 billion.

Even as the bank’s loan modifications imposed heavy losses on investors in these securities, the documents show, Bank of America did not reduce the principal on second mortgages it owned on the same properties. The owner of a home equity line of credit is typically required to take a loss before the holder of a first mortgage.

By slashing the amount the borrower owes on the first mortgage, Bank of America increases the potential for full repayment of its home equity line. Bank of America carried $116 billion in home equity loans on its books at the end of the third quarter of 2012.

Bank of America, the filing noted, “may have engaged in self-dealing and other misconduct, including in connection with modifications to first lien loans held by the Trusts where BofA or Countrywide held second lien loans on the same subject properties.”

Triaxx conducted the analysis by combing through the thousands of loans administered by Bank of America in 530 securities issued by Countrywide from 2005 through 2007. Triaxx then ran the loans through an extensive database it has created of every real estate transaction conducted across the United States during the last decade.

In the aftermath of the financial crisis, investors in mortgage securities have had difficulty identifying improper loan modifications and other servicer abuses like those described in this filing. Servicers have kept under wraps the detailed loan data that could point to these kinds of practices and have forced investors to sue to get access to these files.