Hello sree2005,
I sympathize with your name check hell. Unfortunately, the FOIPA has little consequence or is only partially applicable to the actual name check that occurs within the scope of the National Name Check Program. Now, that doesn't mean that this isn't good to know. Knowledge that their primary databases do not have any negative hits against you is a very good thing, and I don't want to make light of it, but realize that this does not mean that your name check might be processed in the same expediency. Might I suggest that you send a letter to the White House addressed to the First Lady? Its been proven to work way too many times to not notice a consistent pattern wherein individuals who've undertaken this, including myself, have received a letter from the FBI in about 2-3 months informing them that either their name check is cleared, or it has cleared a month or so after (after getting a "in process" letter from them). Its good to know that your wife's name check is cleared. I presume she's the derivative on your application.
Anyway, if it helps, here's a blurb from the FBI itself off their website distinguishing the FOIPA and Name Check:
Freedom of Information and Privacy Act (FOIPA) vs. Name Check: Freedom of Information and Privacy Acts (FOIPA) requests are sometimes confused with name check requests. FOIPA provides copies of FBI files relevant to a specific FOIPA request. For FOIPA, the FBI search uses the name or information as provided in the FOIPA request. A FOIPA search determines whether there is an investigative file associated with an individual—a “main file” search. For a name check, “main files” and “reference files” are both checked, in addition to searching a name in a multitude of combinations.
Good luck and if you're looking for letter templates for writing to the First Lady, a search on these forums would supply you with several.
Regards.