I'm afraid they might be telling the truth. It's not uncommon for this to happen and is not necessarily the fault of agents. Since July 2005, when the previous law was suspended, a backlog built up at the military offices responsible for deciding if you are a suitable individual and that the land on which you want to buy meets Turkish legal requirements.
The military checks were supposed to have become something which local land registry offices carried out , based on military information, but this hasn't happened yet. As a result, there is scope for genuine delay but beware of the agents who don't bother to apply for your deeds for you. Make sure that this is part of the service before you engage them and get any agreements/contracts in writing in Turkish and English.