Did you see this in the FAQ?
"The auto door-locks are driving me crazy. How do I make them not automagically lock the doors? - Shut the doors and turn the key from "off" to "on" (stop turning the key at the point just before the engine starts). Do this five times. On the fifth time the key should be in the "on" position, push up on the power door lock.
To set for all doors to unlock together, follow the same proceedure, except press up on the power door lock 2 times."
Might try the second one and see if that will cause the doors to start locking again. I like it because when you open the door, all doors unlock. Makes it much handier since I usually have something to go around and get out of the passenger seat or the back seat.
2007 Jeep Wrangler Sahara Unlimited
Factory: Silver w/ black soft top, 18" wheels, auto
Mods: Windshield mounted Hella FF1000 driving lights, Rugged Ridge front grab handles, CLC rear grab handles, Teraflex 2.5" BB, Quadratec boor handle covers, Bestop spare cover, Custom front bumper, 17X9 Pro Comp 1079's, 305/17/R17 Buckshot Mudders.
In the works: Custom rear bumper.