I can feel for you. I have an alarm/autostart combo installed just before Xmas, and I have gone back to the installer 4 times to get the new alarm/autostart system to "interface" with the factory alarm properly. Not only I had problem with arming/disarming the factory alarm, I had problem locking/unlocking the door using the p-lock switch (but no problem when I use the remote to arm/lock or disarm/unlock). The installer must have spent over 10 hours working in my X.
Finally, he got everything to work except for the "ignition control door lock" = this feature locks all doors when they are all closed and when the key is in the ON position; and unlock the doors when the key is turn back from ON. For some "highly technical" reasons, he could get this feature to work with the rest.
I watched him worked in my X, and he worked hard and tried many things (under the hood, inside the door panel), but no luck.
Well .... so be it, I am tried of going back.
Besides that, everything works jut fine. The autostart is great, it is lovely to get into a warm car with warm seat, a must for central Canada.