Yes, they do, although sometimes it doesn't show up that way for whatever reason they have for being inconsistent. Sometimes people's never update, sometimes only some (me). I'm sure the letter they give you is right and you can make them update it correctly or dispute with the CRAs.
What you might find most helpful is the IDR details on how they calculate it. You see, you can use your tax information, which most people link to the IRS. But you can share use paychecks, etc. Because some paychecks vary, you can often time it to get the payment you want. So let's say you have a higher than normal paycheck, one that will take you beyond $0 payments. You could use that. Do you mortgage, then recertify later with a lower paycheck to take the payments back down. This is completely complaint with the fine print on the IDR application. However it would have to be a recent paycheck.
Option 2... Pick an Income-driven repayment plan with a higher payment (temporary). It will still be low, but it won't be $0. REPAYE and IBR will probably be the lowest.
It really depends on your martial status for IRS filling and income as to which plan might be low but not zero. You might be able to call Nelnet and ask if they could give you an estimate over the phone or to get close, use the online payment estimator on the student loans gov website.
Does that make sense? Feel free to ask more questions.