The first thought that comes to my mind is that you don't have enough calories in to sustain the amount of exercise that you are doing, so your metabolism has slowed down to conserve the resources you do have. The conventional wisdom seems to be that this happens below about 1200 cals per day for women.
Is your nutritionist aware that you are only consuming 1000-1100 cals per day? Has he/she ever suggested upping the calories?
I would definitely agree with the nutritionist that more protein is preferable to more carbs (don't get me wrong, I have a love affair with carbs, but reality is, well, reality), especially with all the weight training. Carbs will give you energy so eat them before the workout, but be sure to go heavy on the protein after.
Keep at it, and congrats on your loss so far and your dedication in the gym!