ford flex factory alarm disarm

I just did a 2010 Ford Flex the other night and the factory alarm disarm wire did not test right. Neither the Blue/brown or GREEN/ purple from the door harness drop to 0 while turning the key in the drivers door. I does have a factory alarm and also has a keyless entry keypad on the door. What is even more weird is the fact that turning the key in the door doesn't disarm the alarm... Any ideas?

hi, the factory alarm won't disarm with the key in the door. it disarms with 1. pressing Unlock on a programmed remote/key, 2. using a programmed key cycled to RUN position, or 3. entering correct unlock code on door keypad. info obtained from Ford. mark

So how does one bypass the alarm for aftermarket remote starts? I have found that the remote start does bypass the alarm because it starts the vehicle, but I cannot get it to disarm with the aftermarket unlocking.

disarm by method two...trigger bypass module and ignition input, can't determine if special timing is required. diode isolate the bypass ground while running input and extra ignition output relay connected to the remote start disarm output.