2006 jeep grand cherokee laredo rs

Is that an Omega add-on remote starter? If so, the key fob is disabled while its running. That is normal and like any other add-on/upgrade remote starter. You put the key in the door  to unlock it.

Cant answer the OEM alarm problem. I never worked on a Jeep before.

This is what I learned from tech support:

This is not exactly what I wanted to hear about the product they suggested was most suited for chrysler / my vehichle.

I tried programming my CHALL with the instructions from tech support and I still can't keep the factory alarm from being triggered.  Programming the feature above should cause the CHALL to unlock the doors before remote starting and then lock the doors back.  After programming the feature the doors lock after remote start but they do not unlock before remote starting. 

Any ideas, did I get the wrong programming instructions?

Also, I've been pressing the keyfob unlock button manually to disarm the factory alarm so I can at least use the remote start.  It works most of the time but sometimes the accessory circuit only comes on for a moment and then goes off.  Also, when this happens the engine light comes on the next few time I drive.  Seems like something is going on with the MUX wire since this is also the accessory wire.

Any ideas on what to troubleshoot?