I had a similar situation a couple of years - had rented an apartment through one of the big agencies, dealt with them for first lease and agreeing second lease, paid them the deposit although the cheque was made out to the landlord.
at the end of the second term the agency also referred us to the landlord to discuss the depoist - I think this is because they are letting agents rather than management agents so they simply hand the money to the landlord and charge them a fee.
In our case we made a number of calls to the landlord and were promised a cheque was on the way a couple of times, he seemed to keep forgetting about it, so we sent an SAE and got the full deposit back the next week.
so there may not be anything sinister in their agent not dealing with the refund, your friend should contact the landlord asap