For what it counts, that whole carlories in < calories out is total bullshit. It may work for some, but not for everyone. My last year in the Corps I was trying like all hell to drop about 15-20 Lbs. I was eating less than 1000 calories a day, and burning between 2000-3000 a day. Ran at least 5 miles per day, then weight training each afternoon. Never lost a fucking pound that way. I got out last year, and once I started eating again, like LOTS of lean meats, and managing the types of carbs I was eating, reducing the amount of exercise, the weight fell off. I dropped almost 20Lbs in less than 3 weeks eating like this. So yeah, 5 meals a day, mixture of lean meats, minimal veg, little fruit, and good carbs, and yeah, my metabolism finally started working and the weight fell off.
Everybody's body is different, if you're stressing about losing the weight, your body's "fight or flight" will kick in, even minimally, and it shuts down your metabolism. Your body doesn't know the difference between a fearful situation and day to day stress, which is why people in high stress jobs are almost always overweight. Take it for what it's worth man, but it might be the stress that's killing your metabolism.
Sounds like your body was in starvation mode to me. You need to fuel it with enough energy to get through the day and workout if you are working out. By eating more, (but still working out a lot) you have reduced the deficit of your TDEE ie. BMR = 2000, exercise = 2000 so TDEE = 4000. If you are eating 1000 cals a day then you are at 3000 cal deficit per day or 21000 per week. THis is 6lb's of fats worth. Your body is not going to want to drop weight that quickly.
If you upped your cals to 3000 and had a TDEE of 4000 then this is 1000 deficit/day or 7000 per week which is 2lbs of fat per week which is more obtainable.
(I know that when you are losing weight it isn't 100% fat but this is just a simple example)
For the OP: sounds like you are exercising plenty so unless you are not eating any food (like the above example) then I would be reducing the amounts slightly. Go to myfitnesspal.com and log a few days to see where you are currently at and what you need to adjust. You may find the amount of cals in various foods surprising