Of course they won't pay your tuition if you are pending a waiver. If your waiver is denied you will be on the hook for your school bills. Your tuition doesn't get paid by the Army until the 45 day mark anyways, and you actually have until the end of the semester to get your waiver and have the Army pay your bills (you may not receive retroactive stipend). You may have to front your tuition money and get reimbursed depending on how your school feels about trusting the Army to pay up after the 45 day mark. CJS is ight about calling your ROTC Battalion. They will be able to tell you what the deal is at your school.