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Has it been "Charged Off"?
How are they reporting the lates? any 120's? How many months did you skip on the payments? Trying to figure this out.
Have you communicated with them? Asking if they would consider re-opening the account? I'm not sure why your scores would go down if you paid it off? Your UTI will decrease. It would be a whole lot worse if it were to become charged off. 30 days lates start having less effect on your scores as time passes. The 60's and 90's will hurt for quite sometime. You may want to get them to re-open the account and work on GW'ing them for the lates later.
Good news: It's not Charged Off. You're making payments. Worst offense is 90 days late.
Bad News: 90 days late appear on your report. 60+ lates sting. Bad. But not NEARLY as bad as Charge Offs. Those just plain suck for 7 years straight.
IMO: Keep paying and don't stop till its zero balance. THEN... Get another credit card (shop around, use the forums). Build a positive history. Goodwill NFCU to consider deleting 90, 60, whatever they agree to delete. Continuing to pay and get to zero balance WILL be getting it right with them.
That card is showing near "maxed out". Pay the card and your scores will increase.
Congrats on making the decision to become debt free. I'm doing the same thing on a smaller scale and am focusing solely on funding accounts in the next couple of years.