I really, deeply believe that it's damn near impossible to really count calories with any sort of fine precision, due to variable in food (water count and so on), instrument error, and user error. All these problems are compounded when trying to determine calories burned. I do think it's possible to be consistently inaccurate in one direction or another, and so your best strategy is just to stay with what works and if it quits working, try different things.
That said, if you are putting on muscle, you aren't burning it--are you putting on muscle? If you are, and are losing like that, I'd keep at it. If you haven't seen any new muscles after 4-5 weeks of that much exercise, I'd eat more, especially more protein. (I don't mean you should be bulked up, but you should be able to flex your leg and see/feel things moving around in a way they didn't before).