Are the doors unlocking when the horn sounds? Or are they trying to lock again? Maybe your remote is sticking. What does the other remote look like? Does it have a single button? When I got my Commander it had a second remote that ended up being a remote starter. If it only has one button try pushing it for 2 seconds release for 2 and push it again for 2 seconds. The lights will flash and it will start if it's a starter.
I've never heard of a lojack with a remote.
2006 Jeep Commander, 5.7 Hemi, OME 2" HD Lift,Robby spacers,New and improved Jeepin by AL UCA,265/70/17 Fierce Attitude on XD Spy 17x8 with +18 offset,Magnaflow Cat Back,4xGaurd Matrix w/hoop,Mopar Chrome side steps, Chrome door handles,Chrome Fuel door,Chrome Jeep bug deflector,AVS window vents,Home made roof lightbar, 2009 Mygig with lockpick,Backup camera.