I suppose it depends on the school. In my case, the answer was yes, including monthly late fees since the Army always paid 1-3 months late. I was always able to get the fees waived with a couple phone calls, but it got to be annoying after 8 semesters.
The military will cover all late fees and interest if it can't meet the time requirements of the school. Paying tuition is a frightful process regulated by goventment contracting rules. the money will be paid and if your financial aid is held hostage, contact your program and they will get that fixed.