I have several problems with the HVAC system on my '99 Grand Cherokee. First off, all the doors (blend, recirc, defrost) make loud clicking and squeeking sounds when operating (I just replaced the blend and recirc doors and motors). Second, the blower motor is intermittent (Checked the plug and voltage is fine). Third, all the passenger side controls are opposite of what I set on the controller (The recirc door opens when the controller says its closed and vice-versa, and the passenger side gets hot when set to cold, and cold when set to hot. The driver side is fine). The only fault codes I get are for the blend and recirc doors over-travel.
In (hopefully) unrelated news, my radio randomly loses power at times (started after I got a car wash and they removed my antenna).