I didn't see any mention of AOTC. Under the assumption that you are NOT eligible for that tax credit, there really is no reason to input the 1099Qs as all. You've already proven that none of it is taxable based on the analysis that you'e provided.
Look closely at the instructions on the 1099Q - you are simply required to determine the distributions are not taxable; it is not reported to the IRS in any event. Nothing in Box 2 is taxable because your qualified expenses exceed Box 1. And those can be done in summary as you have multiple 1099Q. might be an easier approach.
if you are eligible for AOTC, then up to $4000 of the expenses off the 1098T is consumed to yield the $2500 of tax credit. That could be why the expenses are being adjusted.
Can you comment back on whether you are eligible for AOTC and I can take you through the math?
