Are you eating a lot of bars? They're sweetened with maltitol, which bothers some people. If you weren't eating a lot of fiber before, that could be the culprit also. If it's the fiber, it should improve; if it's the maltitol, probably not.
For me, the gas never really got better (or at least not yet) but then I don't recall having a big problem with it the first week. (It really started up for me after a couple of weeks.) So, hopefully for you, its just your system adjusting and it will settle down soon.
I don't understand what is causing the gas. I only eat 1 bar a day and my counselor helped me pick out the products with the least soy. I take the enzymes they gave me but they aren't helping. I paid up front at the center and will tough it out but the gas is embarrassing!
Medifast products contain fiber--that might be the cause. Some people do get gas with certain kinds of fiber supplements. If that's the cause, it may get better over time. It may not be the soy at all.