After deducting the reservation fee, did they refund any of the rest of your deposit?
I can understand the reservation fee...that's pretty common, and I think that just about any of the local companies would still charge it. Haven't a clue why they would keep any of the rest so far out.
Do keep in mind that your being a repeat customer may not be apparent (unless you told them). Property management personnel change rapidly, and records from three years ago are not generally readily available. At least they aren't when I ask for them.
Good luck -