i had the same exact thing happen on my cutt when te engine was replaced. the vent selector switch is vacume operated and when they replaced the engine the vacume hose in the engine bay was not hooked back up. it would only blow through the top and bottom vents. i tapped it back in and now it works fine.... good luck.
by the way, the easist way to tell if it has vacume is to turn it on/off from max a/c. the vent door behind the glove box should open/close.