New York likes to do things its own way. So when the U.S. Treasury Department began implementing a new housing bond program to help revive housing finance agencies hurt by the mortgage meltdown, the state’s biggest issuers of such bonds wanted to adapt it to their own business models.

The result has been a headache that the New York City Housing Development Corp. and the New York State Housing Finance Agency hope is lifting after much negotiation. Even so, without an extension of the New Issue Bond Purchase program, it’s unclear whether the issuers will be able to use their full bond allocations under the program by an end-of-the-year deadline.

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