I am having trouble with the education credits. I believe, as a grad student with income less than 7K and only a small $650 scholarship I qualify. Can someone explain?

I graduated undergrad in the spring, paid about 3K in tuition (this shows up in box 1 on the 1098-T) more than half-time student.  
I started grad school at a new school as a more than half-time student and paid tuition with loans and small scholarship.  Tuition and fees of about 6K show up in box 2 on that 1098-T form.  I am not sure why, but there is no value in box 1.  In the program I selected "but this isn't the amount I paid the university" and entered the amount I paid with loans, scholarship and savings in that box.

I have an income of less than 7K for the year and had to take out loans to pay for tuition and living.  Am I wrong? Do I really not qualify? or is it possible I or the program screwed up?  If so, how do I fix this?
Thank you for your help!  Trying not to rip my hair out over here!