When i had my tailgate apart to install the keyless entry, i broke the vacuum lock actuator for the tailgate lock...the odd thing was that while i was waiting for a new lock actuator to arrive, i tried to use the keyless entry system. it worked to unlock all of the doors [obviously not the hatch] but would not disarm the alarm system. once i put the new actuator in the hatch, the alarm would deactivate when i used the keyless entry. the only thing that i can figure out is that the alarm gets its signal from the lock itself, not the hatch actuator; even though the hatch actuator has a harness section plugged into it...if you open up the tailgate, your alarm problem should be somewhere on the passenger side of the lock itself. sorry that i can't provide any further info, but my new actuator solved my problem...
