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Their system is weird that way. I just make a monthly payment regardless, I don't pay the minimum payments anyway other than having that weird zero there it is not an issue.
With USAA it's possible to opt-out of what they refer to as the 'Pay Ahead Program', so it might be possible to opt-out with NFCU as well (I'm not certain). This might make sense if somebody has a bill pay service that is triggered by a minimum payment being due rather than a balance. Keep in mind that if you're carrying a balance that interest will continue to accrue even if there's no payment due.
In my case I like this. In the past I once made the mistake of making a payment just before the due date on a student loan; in that case they didn't have a 'Pay ahead' setup so that payment was counted as an additional payment on the previous month and a few days later I still had a payment due (times were tough then, and this was a real setback). The way NFCU and USAA have things set up a slightly-early payment is not a problem. (Also, note that with USAA they will allow a large payment to go towards up to the next two regular minimum payments; I'm not sure what the fine-print says with NFCU).
Interesting. I'd send a proper payment anyway just to be 100% safe.