Food intolerance and weight gain

Does anyone have any experience with weight gain as a result of food intolerance and perhaps losing that weight after you identify it?

I've been consistently, steadily gaining weight since February. I'm back to where I started-up about 12 pounds. I've been working out the same (if not more), added strength training, and eating healthy. And it's not a gain of muscle--my pants do not fit me AT all. I've been at net 1,200 calories now for awhile, but with exercise, I on average eat 1,500 to 1,600 a day, so I'm not in starvation mode (tried eating more and less, nothing works). Plus, I lost at that level before, but now I'm not only not losing, I'm gaining.

I thought it might have been an effect of going off a BCP, but I'm bloated all of the time and have just generally felt lethargic, ravenously hungry (I am eating protein and fiber!!), and dealing with weird food cravings. I got my thyroid tested, as well as a lot of other things tested (including Celiac's), and so far, nothing is abnormal. My dr suggested cutting out dairy for a week, which I did, but I don't know how well (traces of milk in stuff that I didn't realize were there), and then reintroducing it. I didn't notice a huge difference in the way I felt without dairy and I'm reintroducing it now and will go off it again to try again. But I'm wondering what kind of other food intolerances there are out there and what else I could try.

Thanks!