sunrise, are you sure it was Fannie Mae's system and not Freddie Mac's? Fannie Mae is OK with disputed accounts (I'm actually doing several loans for clients who have disputed accounts), but Freddie Mac would not accept someone with a pending dispute.
glassblower, for the best conforming rates, when putting less than 30% down, it's best to have a 680+ mid score from all applicants. It definitely think your wife's scores should see a nice jump when that mortgage balance is reported as $0 and the past due amount is removed.
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