Jim in your example you said: "Since scholarships are greater than expenses, it is considering this unearned income ....". I don't believe that is correct. Taxable scholarships are reported on line 1 (Wages) of Form 1040.
I don't know any way around your problem. It appears that not all Universities complete form 1098T in the same way. My daughter's University completes both Box 1 and Box 5 on a calendar basis.
