Ann:
The online system that tracks federal loans is called NSLDS. It tracks all federal student loans and grants that a student has received. You can access this at www.nslds.ed.gov using your PIN. I have worked in student finance for over 8 years for several for-profit universities and believe I know exactly what happened here. If you attend a school past the first week, they will charge you for classes and depending on how long you attend, it may be the full amount. This is the policy of any school you choose and is typically spelled out in their catalog. If you drop early in the process, you may not be entitled to ANY financial aid and could owe the school hundreds (or even thousands) of dollars. Secondly, any loans must be certified before your official last date of attenance. If your last date of attendance was BEFORE the loans were certified, the loans have to be returned to the lender in full (but you will still be charged for the classes). The financial aid refund schedule and the school's tuition refund policies are not the same, and that is key.
Finally, schools must issue a refund to a student within 14 days of receiving federal funds (title IV). However, if you drop out early in the term, drop before the loan certification date, or drop below 6 credit hours, you may not be entitled to these funds. Since there is usally a processing delay between the time the funds are received and any drops entered, you could receive a refund even though you are not entitled to it. This is why the financial aid advisor called you so urgently. It necessary for you to return the funds to cover your tuition charges and/or the portion they need to return to the lender (if any). The transaction fee you are referring to is the origination fee the lender charges (not the school). It sounds like in the end the school did not withdraw you from school, instead giving you the F's which may have been a better option if the other option was to have you owing hundreds or thousands of dollars by returning all the funds to the lender. This may not have been the correct thing to do on their part, but you could be on the hook if they had dropped you early on.