Open hood. Start engine. Switch HVAC control to front windshield defrost setting and turn fan on. Can you hear the air conditioning compressor cycling off and on? If should be putting a light load on the engine and an audible thump when clutch engages and disengages.
Also try turning HVAC control to A/C and then turn the rear HVAC to cold. Are you getting cold air back there? After running this way for a few moments, are the silver A/C lines under the hood getting cold/sweating?
Do you have the optional electronic dual-zone climate control? Any noise from under the dash, like a clicking noise?