Form 1098-T Box 1 seems to be calculated as the TOTAL cost of tuition versus the amount we paid for tuition.

[macuser_22]

From the 1098-T instructions:

Box 1. Payments Received for Qualified Tuition
and Related Expenses
Enter the total amount of payments received for qualified
tuition and related expenses from all sources during the
calendar year. The amount reported is the total amount of
payments received less any reimbursements or refunds
made during the calendar year that relate to the payments
received for qualified tuition and related expenses during the
same calendar year. The amount reported is not reduced by
scholarships and grants reported in box 5. Include in this box
the receipt of a payment of past-due qualified tuition or
related expenses from a previous calendar year, but only if
the educational institution previously billed the student for
such amount(s).

If that is not what is in box 1 then contact the school that issued it for a corrected 1098-T.

[Hal_Al]

You claim the tuition credit, or report scholarship income, based on your own financial records, not the 1098-T. In the 1098-T screen, click on the link "What if this is not what I paid the school" underneath box 1. You will then be able to enter the actual amounts paid. 

Or if you find it easier, just change the number in box 1 to what your records show. The 1098-T that you enter in TT is not sent to the IRS.

[Carl]

That is correct. Box 1 shows the total amount paid for tuition and other "QUALIFIED" education expenses from all sources. Whereas box 5 shows the amount of money received by the school from all third party sources. If box 5 is the lower amount, then the difference is the amount paid out of pocket.

If box 5 is the higher amount, then you may not qualify for any education credits, and the student will be taxed on the excess third part funds received.

Keep in mind also, that box 1 does not always include all qualified education expenses either. That's why the program will ask you for such expenses that were not included in box 1. Same goes for box 5 too.