Can' t say for sure what your problem might be but I can tell for a fact that not eating at very least three meals a day is the Absolute WORST Thing you can do!!!
First this is true because your body needs the proper fuel to be healthy anyway.
Second since you are an Athlete not eating can be even more detrimental to your health. Your vigorous work-outs are causing your body to use more calories than other people with normal rates of exercise do. That means if your body does not get the proper nutrients it needs from the food you take in to your body it will find a way to get the nutrients elsewhere.
What that means is that it will start to eat the nutrients in your Muscles! Which I am sure you can guess is very very very bad.
I sincerely hope this is not the case with you but I do know that malnourishment can actually cause your stomach to get bigger over time. Have you ever seen those pictures of starving children in places like Africa with the big stomachs? That is because of malnourishment since they do not have enough food to eat.
You said you drink healthy so I am guessing you don't drink a lot of beer because that can also make your stomach get bigger.
But since you said you only drink healthy that worries me because most people say they eat healthy so I wonder if you are eating at all? Please eat normal amounts of food and if you are really worried that something may be physically wrong with you see a Doctor to get help. And be honest with them about your daily habits of exercise and not eating properly and see what advice they give you.
So bottom line eat healthy and maybe try a few less workouts for a little bit and see how you feel.