How long did you pre-heat for? I'd give a regular pizza stone at least an hour, probably longer to be honest.
You'll get better (and quicker in terms of pre-heating requirement) results by using a cast iron or steel pizza "stone"
edit: Based on your pizza pics (which looked awesome, especially the pepperoni) in the show off your dish thread I'd probably suggest flattening down your dough a little more. Possibly using less dough in fact. You may also want to try switching to grill mode a few minutes before you stick your pizza in to get a browner top too, though that won't work too well with a regular pizza stone - you'll need the cast iron or steel stone I talked about for this to be practical.