Need help figuring out what to do with program (Long sorry)

I am going through a weight loss program offered through the local hospital. It includes prepackaged food and weight loss classes. The classes have proved interesting at times, but more often than not just remind me of what I already know from college level nutrition classes, common sense, and not having my head stuffed in nether regions. The classes do provide a certain level of accountability but I think I'm going to cry soon, (too late already did).

I don't know if this is the program I should be in, and trying to use myfitnesspal has made me even a little more crazy that I would be without. The main reason mfp makes me crazy is because it adds calories to my diet if I work out. I tried that, even filled it with good for you stuff, my thanks I gain 3 lbs. So I stuck with their diet only, and mft is constantly telling me I didn't reach my food goal. Which actually becomes annoying and now I'm wondering who or if anyone is right, and what should I do.

I want to get healthy, I want to lose fat, but losing fat does not always equal to losing weight. Here is what is going on.

In the month of June I went from 206 down to 189,or 186ish. Although I lost near twenty pounds my body dimensions lost less than an inch. At the beginning of July once I was measured for BMI with a hand held device and calipers my BMI was at 42.5% which is higher than I had ever thought.

Here in July I went from 186, to 181 after I started working with a trainer at the gym.. However, I have dropped from a 42.8 inch waist line to a 37.75 inch waist, my hips went from a whopping 47.5 to 44.25. My BMI has dropped from 42.5% down to 39%. I want to lose the fat, it is going to kill me, by gaining muscle it will help insure that I keep the fat off. When weight is not mentioned I personally don't care if the scale creeps down or suddenly blast off as long as the other measurements keep dropping. This Is due to the extreme work outs I have started doing that can include 30-50 min. circuit training, 30-45 min on elliptical, 20-40 min on treadmill walking slowly to make sure I clear out all the lactic acid and am not in pain after working it that hard.

When I calculate my heavy work out days that happen 3-4 times a week using my fitness pal, I burn anywhere from 900-1300 calories. On the other days of the week I burn about 600. I stay on the diet, when I have my dinner protein that is different I will say 90% of the time it is with light fish. I can send you some pretty pics of dinner plates full of color and slammed full of food, not to mention a cup of soup I often have with it. My average calorie consumption is around 1000-1100, yes I actually exercise away more Kcal than I eat several days a week. I have more energy, less joint pain and feel so much better. It looks like my high blood pressure is something that has already got lost somewhere along with the inches I lost.

I don't know if that significant of a calorie deficit is ok. Before I work out I have a protein shake with fruit, often with so delicious sugar free coconut milk that has like 45 Kcal. After working out I normally drink a shake with fruit while still at the gym waiting for my body to regather itself. I come home eat a lunch that consist of an entrée or fish, a salad with tomato's, cucumbers, strawberries and fat free dressing, and about 2-3 cups of something like a summer squash, bok choy, stir fry veggies, broccoli or what ever other veggie I desire. It will come up to about 300-400 Kcal sometimes a little over 400 and I'm done. I then am just thirsty for the rest of the day. I drink enough water to float down a river, but a lot of stuff just seems yucky. I mean I don't want another entrée I try but swear half way through I'm going to vomit. I try the shakes, but they seem gross, and I don't want any of it. I'm not a big soda or Ice cream person so mimicking them doesn't really help. The cappuccino goes down but I don't want to over do caffeine. Some days I find myself eyeing a piece of bread even plain without butter, just anything with carbs. Which I would never do before. But then other days like yesterday, I worked my tail off with my trainer then did the standing elliptical for the first time without my knees hurting and a few other things ended up burning over 1300 Kcal at the gym, by the end of the day, I had only eaten 790 Kcal, but I threw away two shakes, and an entrée because I just couldn't stomach it.

With all this I have only lost 6 pounds, I know I'm gaining muscle, losing fat, dropping my blood pressure, pulse, and getting healthier. I also know my uterus is literally working against me. With the ultrasounds they discovered right after my cycle it is about 3x the normal size, by day 12 of my cycle it is 7x larger than normal, I told them I didn't want to know what it was like when I was even closer to my cycle starting. This finding explains some of the large jumps we have seen on the scale, I don't know when me and the Navy are going to end our negotiations on me not seeing one of their providers, so it may continue this way for a while. So there may be only one even close accurate measure of weight a month, the one right after my cycle ends.

I don't know if focusing on "weight loss" is primary for me right now. I don't know if staying in this basic class is good idea or or just somewhere else. I like what I have learned and the support, but I honestly look at numbers that we use "veggies, fruits, entree's, water, MTG (movement target goal minutes exercised x8 = mtg ) and concepts like calorie deficit = weight loss is not working right in my world right now, and it makes me want to scream because I'm like hey I'm doing that but it doesn't work that way for me. I feel like it is ethically wrong to speak up in class and say, "Well, I blew the roof off my MTG and hit 4400 for my MTG, and yes I'm eating 5 entrees, 4 other proteins oh those missing ones, well I didn't eat them because I tried and thought I was going to hurl. I did eat 25 vegetables, and 16 fruits this week, and oops sorry I drank all the Pensacola water supply and I only lost one damn pound." Or the more joyful answer or "no, I actually gained weight this week, because my weight is diet resistant".

Any suggestions or am I fine right where I'm at?