Just a nit-noid fact, in case if prevents any confusion while you try to fix this. "Freon" is a brand name for R-12 that is banned and no longer used, your Jeep uses R-134a for its refrigerant. It's like "Clean-Ex", "Q-Tip", "Kevlar", the popular brand name "Freon" gets misused as the name for a catagorie of product. So, use the words "refrigerant" or "R-134a" as you talk to techs or auto store folks so you don't create any confusion, or give someone with an attitude problem an excuse to look down on you.
When you say HOT? Do you mean the air is heated from the heater or just NOT cooled at all and it is the same temp as the outside air.
The environmental control units have small electric motor that turn plastic shafts to open "air blend" doors to direct the air, either over the AC evaporator and/or Heater Core and then out to different vents. So, if you have a good working AC system, the motors/shafts or doors of the "air blend" doors failing could cause it to blow hot or non-cooled air.
When the air blend doors fail, it "can" cause bad direction of air to the point it is NOT blowing or flowing from the vents you select or barely flowing from any vent even though the fan is whirring at full speed.
The Front and Rear AC/Heat are seperate units with their own doors, so one failing would NOT make the other fail.
BUT, you mentioned the compressor going constantly cycling between on/off, air blend doors don't cause this.
This is a classic symptom of being low on refrigerant. And the only way to be low on refrigerant is too have a leak.
My evaporator developed a leak, I've seen posts for other evaporators leaking on this forum (as well as air blend doors breaking), so it seems the front evaporator leaking is NOT uncommon on the Commander.
A leaking evaporator in the front would cause it NOT too cool (at least cool poorly) in the front, but the rear evaporator would still function while there was still some refrigerant left in the system (and the rear would get worse as the system leaked down).
Sorry, but to replace the Evaporator is a big job, the entire dash has to be pulled out. I just did it myself, it took all weekend, I'll have to post some pics I took. So, this is going to be an expensive repair to have a shop do it, NOT that the evaporator itself is cheap either.
One thing to keep in mind, AC oil. While the evaporator leaks, it will also leak out oil. If you keep recharging the AC with store bought cans R-134a, but NOT replacing the oil leaked out, you will run low on oil and that will cause your compressor to seize. That happened to me, and my AC repair got a whole lot more expensive.
The Commander's AC system uses ND-8 oil, which is the same as PAG iso 46 oil or PAG46.
The best thing to do is just get it repaired right away. You keep using the AC with a leaking evaporator, you're asking for trouble. But, if your going to keep recharging it with cans of R-134a yourself, then buy some cans of oil while you're at it and keep adding oil.
BTW, I Don't Know if your problem is really a leaking evaporator, from what you tell us, the symptoms sound like it, but I could be wrong, please take it to a shop and have them diagnose the problem for you.
A leak anywhere else in the system would cause both front and rear evaporators to perform equally poorly. The front expansion valve failing would cause the front to perform poorly while the rear performed better, and those parts can be replaced without tearing apart the dash, but you wouldn't have symptoms of being low on refrigerant.