I would take the enzymes just before eating. For example, in the morning, I take my enzymes, and then I cook my eggs. How is your fiber intake? I can't place where I read it, but supposedly the longer food is in the lower half of the digestive tract the worse your gas will be. So if you get a good mix of soluble and insoluble fiber, this combo will slow things down at the beginning, thus lowering the GI of your meal, but it will also speed things up on the "lower" end, pushing things through so that excess gas doesn't build up.
I just recently bought more ON whey, and I've noticed an increase in gas again. Once it is gone, I'm going isolate only. I definitely think this makes a difference.