I had a really hard time reprogramming mine, after originally doing it in two minutes. Mine failed the other day, and stubbornly would not reprogram. I am including the correct instructions beleow, that you have probably tried. Just take your time, it is extremely inlike BOTH of your FOBs failed. Try these things. Program with door open, try again with it closed. Make sure the LED on center console is blinking, else you are not in programing mode. Make sure you program 5 devices (even though you physically have only 2. I suggest 1 beep on one, and 4 on the other (or just do 5 on one, and save the other as an unprogramed spare. Also, try skiping the "hold brights while switching to position 1 with key". Also, MAKE SURE you are in position 1, not 2 as that will not work. Be persistent, if it fails, try again later. I tried about 10 times and failed. Went back several hours later, and it programed right up. If you are hearing a double beep after about a minute, it is telling you it did not program. That's all I can think of. Oh yeah, also, you can orogram the FOBs to the memory for seat,mirrors and headrest positition (only after programing it to the car first. To program it to memory: select the memory button, then a memory position button (1 through 3) and finally press lock or unlock on the fob within a couple seconds. You should hear a confirm tone. Very cool when you have it set for more than one FOB, and more than one driver.

Here is the "official" method that worked for me, even after being stubborn one afternoon. Maybe it matters what state the cars locks are in, I would try experimenting with that too (locked, unlocked, just drivers door unlocked etc. Remember this is a PROGRAM, and a PROGRAM needs to follow rulesets. Good luck, and let us know when you succeed (and you will)

correct
instructions for a 99 XJ.

Note : All RF handset transmitters belonging to the vehicle being serviced
must be available. If the learning process is carried out without having all
the transmitters present, all previous transmitter codes will be
overwritten, rendering the missing transmitters inoperable.
Hold headlight flasher back.

Turn ignition key to position 1.

Flash headlights 4 times.

Alarm will enter programming mode.

This will be confirmed by "beeps" from the alarm and flashing led on
gearshift.

Program each transmitter (up to 5) by pressing the lock or unlock button on
the each transmitter once.

The alarm will "honk" when you press the transmitter button.

The alarm must honk 5 times to complete the programming. Therefore, if you
are only programming one transmitter you should operate the transmitter 5
times. If you are programming two transmitters you will operate one
transmitter twice, and three times on the other. For five transmitters you
will operate each transmitter once.