Since you posted on the Thick Style board, can you describe what you mean by "stuffed"? That is, is it like a stuffed deep-dish pizza, or something else? If the latter, please describe how you construct the stuffed pizza.
Also, what kind and brand of bread flour are you using, and how do you measure out the three cups from your flour container? There are many different ways of doing this, and knowing your method might help address your problem. And what kind of milk are you using, that is, whole milk, nonfat, part-skim, etc.?
Finally, how specifically are you baking the pizza--in a pan, on a screen, on a preheated pizza stone, or whatever?