Could be the Vacum lines that switch the vents? (Now I cant remember if it uses a vacum or a cable? But I already typed this)
I can test later on my '97 but I am almost certain that if you have the Jeep running with the blower on 1 or 2 - move the bottom heat-slider-thingy (don't know the name of that slider) from Hot to Cold. As you move that you should hear a change in the sound of the air flow coming out of the vents.
Could be an air bubble in the cooling system?
Did you work/have work done on any part of the cooling system?
Is your Temp on the dash reading "normal?"
Let us know pal.