Thats really weird...You say that you think its working when you manually lock the doors cuz the LED comes on...if you unlock the door with your key the alarm doesnt go off right? I dont know about stock alarms, but on aftermarkets that i have delt with you cant open the door with the key without the alarm going off, so i dont think it activating just becasue the led comes on...

As for the remotes, that is trippy...It even happened on a backup remote huh...try taking the battery out and getting out of range of the car...I wouldnt think the car can transmit to the remote to screw it up, but somthing must be somhow if its screwing up a backup remote...

I really dont know...my stepmom is havin some major probs with her facotry alarm, and i tryed working on it, and couldnt fix it, its been in the shop for a few days...