Seems like what you send to them is N-11 ....which is a State tax return...and that is the reason that your school is telling you that it is a State tax return.
You should fax them FOrm 1040....which is the US individual Income tax return.
Here is the link to how the form looks like.... (You are right about "On a seperate page it even says " 1040 Us individul Income Tax return" IRS use only. I KNOW this is my federal")
http://www.irs.gov/pub/irs-pdf/f1040.pdf
Let me know if you have any question.
renu@yashcon.com
Please note: This advice is provided with the understanding that all the relevant facts have been provided by you. Any change in facts might affect the advice given and hence may not be relied on in such cases.