hard to tell without looking at your swing, but i'll throw in a quickie response with a few questions.
how wide of a stance do you take with your wedges/short irons?
on your mid/long irons/driver, are your feet shoulder width apart? more? less?
when you say problems, what type of shot are we talking about? fat? thin? slice? all of the above?
every golfer has their own preferences, but if i were to generalize, the wider stance could possibly restrict your turn on the backswing, while your short irons/wedges are narrower giving you a more natural body turn. some people need that, some people don't. like i said, could be a number of things.