my husband and I have been zoning for half a year, and no problems, but recently went back to visit the family for a week, and although we did our best, we did have to eat more unfavorable carbs than normal. (Eg: my mother-in-law makes chicken and baked potatoes and to appease us, a bag of mixed veggies, not knowing that each of us would eat our own bag, plus another two for her and my FIL.) Anyway, we did our best, but were eating potatoes, peas, bread, as needed (though in zone-favorable portions).
So... to make a long story longer, we returned home and went to the grocery store, and began, thankfully, eating as we used to, pre-holidays. After a delicious dinner of chicken stir-fry with yellow and green peppers, zucchini, onions, garlic, ginger, broccoli and olive oil, with an apple for dessert, we BOTH had major gas last night! Not really stinky, but uncomfortable. I remember a little of this from the beginning, and know that it very much did subside as our bodies got used to digesting food that is good for us. Water drinking did help a lot, so I would also encourage that, but give yourself time. You may want to also add a mixture of low and medium density carbs to take the edge off. Example--my favorite lunch to take with me to work includes steamed broccoli, whole-rye bread, cheese and ham or cottage cheese, nuts and 1/2 apple. The rye + the broccoli+ the apple is something I can handle, but if I were to eat all broccoli, I think it would be different.
Be patient--it will take time for you to adjust, for your body to adjust, to learn the Zone, and to learn how the Zone works best for you (it's very individual.) When you do, you will reap so many benefits, and likely you won't want to stop! (This was soooo proven to us over this last week! It's so nice to be home and back in the Zone!)