Your question is a little confusing. Please clarify some of the details.
You said "I put them as separate but live together." That's not one of the choices on the FAFSA, and I don't know what it means. Do you mean that in the question about your parents' marital status you selected "Unmarried and both legal parents living together"?
The instructions on the FAFSA say if your answer was "Unmarried and both legal parents living together," contact 1-800-433-3243 for assistance with answering the questions about their taxes and income. If that is the answer you selected, did you call that number? What did they tell you to do?
Are your parents legally married to each other?
Do your parents live together?
What is the filing status on your parents' tax return, or returns?
From what you wrote, it sounds like your parents might have filed as married filing jointly. If they are not married, they cannot legally file as married filing jointly (nor as married filing separately). They have to each file their own separate tax return as single, or possibly one of them might meet the requirements to file as head of household. If they are not married, but they filed as married filing jointly, correcting their tax return is a very complex process. They will need a tax professional to straighten it out for them.
We can answer your tax questions, but we can't tell you why your school would ask for certain documents, or why they would accept something one year and not accept it the next year. It's possible that they just didn't notice the discrepancy in previous years.
