It's hard to say exactly what you may have overlooked. If the vehicle is starting by remote, it does not make sense that the OEM security is still armed. You may have other problems that you have not discovered yet.
The factory disarm wire should be at the BCM: connector 2 pin 9 (lt green w/orange). You will need to send a negative signal to this wire through a 473 ohm resistor and a relay.
If the remote start unit has a factory disarm signal wire use that, if not, use the unlock output from the aftermarket alarm.
Negative signal to relay pin#85, pin#86 to +12V, pin#30 to ground and pin#87 to the 473 ohm resistor the other end of the resistor connects to the wire on the BCM.
I am fairly sure this will work. I have an 06 so it's not the same deal. Good luck getting it done.
