I'm not sure how it works where you are, but Realtors here typically collect the application fee(s) and security deposit with the submission of the application. The application fee covers the background and credit checks, and have to be paid for that report to be run. We usually keep the security deposit (or the listing agent does) until the application has been approved. The security deposit is cashed when the lease has been signed by both parties. The first month's rent is due prior to move in.
Did you sign an approved lease, or is it just the application?