If your scholarship amount exceeds the tuition amount, the difference will be taxable as wages on Form 1040.  If all your tuition is used to pay for tuition, it will not be taxable.  In fact, if you have paid your required education expenses out of pocket, you may claim an education credit. 

I have taxable wages included on my W2 form. The scholarship, given nontaxable status, is still changing my federal return amount substantially - now it suggest I owe federal money rather than receiving a return.

May I know how is your 1098-T is reported? amounts in the boxes?

#1. $60, no value in 2 or 4, #5. ~$20,000, returning full time graduate student, change in school reporting from 2017

So, your out of pocket exp is $60, after using the scholarship, you still have 20k-60 left.  IRS requires the difference as a taxable event.  Scholarship is not always nontaxable.  The portion not used to pay for tuition or books, is taxable.

I spoke with a financial representative from the university. She stated the 20k was reported Jan 8th, but the tuition it applies to was reported on my 2017 1098-T form. She said it is structured this way for potential Education Credits. All the 20k was applied toward tuition, how should this be off-set with the 2017 1098-T?

so how did your report your 2017 1098-T? Did you claim any education credit already?