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I had a similar problem on my 2000 Cherokee. I believe my problem was air trapped in the heater core. I drained and refilled the system, but it wouldn't blow hot.

The small underhood space for the radiator and hoses leads to air being trapped in the system. Factory probably should have installed an air bleed near the thermostat.





Ya got me wondering with that one.
I took the Jeep for it's oil change a few minutes ago. Again, as I got the thing up to temp, I tried the heater. It blew warn at the start, then went to cold fairly rapidly. On the way home I tried it again, pretty much the same thing (only I left it on low, and it almost stayed up with the demand). I sat in the car port with the heater on defrost (RPM around 2000+). On low (fan speed) heat will keep up, and stay somewhat warn. But as soon as I go to med./high back to getting cold (or drop my RPM). Perhaps an entire coolant flush should be done (using a good grade of flush chemical), getting ride of any possibility of trapped air, and some fresh coolant.