Fortuner has a separate blower for the rear AC. The rear AC sucks air from a vent located in the third row on the right side. It usually gets obstructed when brand new plastic wrapped third row seats are folded up. The seat plastic covers the vent and hence, theres no air flow. Just fold down your third row seats and check to see if the vent is unobstructed. If this is the case, your problem will be fixed.