We are experiencing the same problem.
The jeep was working perfectly for 6 months, and one day we nipped into town, got out and the key fob wouldn't work.
We changed the batteries, still no luck. We tried to follow the manual to reprogram them to no avail.
We tried a few garages and all said to go to a jeep dealership, got the car towed there (after much stress) and as soon as it was off the tow truck the jeep guy came and sat in the car and the fob worked straight away.
There had been no problems since until today, where the same thing happened. Got to town, got some bits and pieces, went to unlock the car and nothing.
This time we didn't stress as much, went for a beer and a walk on the beach. And three hours later, got back to the car, the usual fob wouldn't work, pressed the secondary fob and it worked.
Not really sure why it's acting like this.
However we live in spain, in the mountains ( uk 4.0 1997 grand cherokee) , because of where we live, if this continues we are going to be really boned at somepoint.
If there are any tricks to reprogram it so it works without fault, or a trick to bypass the immobiliser completely, could someone please help? It would be much much much appreciated.
Our keyfob(s) are the same ones as posted earlier in this thread.
We don't particularly need central locking or the car to be alarmed if it comes down to it, just need 100% reliability.
I can take any photos needed if neccesary.
kind regards, Ian