Do you have the 4.0L 6? If so, as you face the engine there is a vacuum line about halfway back on the right hand side of the engine. Check to ensure it is securely attached. If it comes off the A/C will not work.
I don't know if this is what you're experiencing or not, but it's worth checking. I also don't know the technical background on what or why, but this small hose came loose on mine and the A/C quit. I reattached it and secured it with a small zip tie and have not had a problem since.