I am also a contractor working for a defense company on a Navy contract. My company requires me to book travel through our company-managed travel site. A couple weeks ago, the FY15 per diem rates were not loaded into the system yet, so our company rate at any hotel selected was higher than per diem.
For an upcoming trip in October(FY15), what I had to do was book at the company rate, higher than per diem. Then I called the hotel directly(Marriott Tysons Corner VA) and asked if they can extend a per diem rate to me even though I'm a contractor and explain how my company has a negotiated rate that is equal to per diem. They happily obliged and changed my reservation to the "Federal Govt rate" that now shows on my confirmation online when I log into Marriott.com They are the ones that changed it to that, I didn't select that rate...
After reading this, I might be printing out hard copies from our travel website that shows our company rate is indeed equal to per diem. And worst case I could call our travel agency and have them rebook the hotels at our rate, which by now should be equal to per diem since they should have loaded it in now.