Just in case anybody else reads this, I thought I would post the solution. If you create an AIR desktop app, but you include a single instance of a MobileSkin to skin an element, the entire app will not display as intended and the scrollbars will not behave correctly on a Mac. Windows is a little more forgiving, but only a little. On a Mac, AIR actually will behave like it is on a mobile device making the scrollbar disappear and applying mobile skins to components like checkboxes automatically making the app look differently than designed.
YOU MUST REMOVE ALL MOBILE SKINS!!! -- Sent from: http://apache-flex-users.2333346.n4.nabble.com/