alarm only works with factory remote

Hey guys I have been working on my alarm install for the last month now. I have a dodge magnum with a bypass kit for the remote start and the doors. Long story short I will get a false alarm on my door trigger if I dont lock the car with the factory key first. If I lock it wiht the 2 way pager remote it will lock then 15 seconds later the alarm will go off. All I have to do is disarm and arm again and its fine. But if I lock first with the key wait 3 seconds then lock with alarm I have no problem. My door locks and triggers are going threw the bypass so no direct wires to the doors. I have a diode on the bypass door trigger but help.

Rewire it so you are using the true door triggers in the car. My notes say the wires can be found in each kick panel. I haven't done an alarm in a Magnum, but I would guess you will probably find the passenger side doors in the pass. kick, and the drivers side doors in the drivers kick. The LF door is purple in the white plug, pin 3. The RF door is PURPLE / white in the white plug, pin 16. The LR door is PURPLE / gray in the gray 26 pin plug, pin 10. The RR door is purple / YELLOW in the gray 26 pin plug, pin 9. Use all four wires and diode isolate each. Trunk pin PURPLE / orange in passenger kick. All 5 wires are (-) trigger.