I have had a similar problem recently, due to the flu, but I had a funny stomach almost all the time till I reached 20.
Sometimes it is the fiber in your food, if you eat a bunch of greens or broccoli or gabbage(or tomatoes with the skin, or peppers with the seeds).
Avoiding spices or those gassy foods may help.
Sometimes it is the way you chew the food, the slower you eat the better it gets.
You can try e few harmless things.
1. First thing in the morning have a shot of virgin olive oil and the juice of one lemon (equal quantities of both). It helps your digestion throughout the day. It is a very common way to address something like that in my country.
2. Drink spearmint/cammomile tea throughout the day and before you go to bed, but especially with meals. If you hate it, you can try broth.
It takes some time to make, but you can refrigerate it and microwave it to drink with meals. Here is a good link about the benefits and how to make it:
http://www.westonaprice.org/foodfeatures/broth.html
3. You can also order or buy some digestive enzymes.
4. Usually adding some fats to your protein helps digest it better. If I eat a dry piece of chicken I also get sour cream with it.
Hope some of these helped:
galya