I recently installed the factory remote start on my 2013 F150 and it all works as it should except I cannot turn the truck off with the key fob. I lock the truck and press the start button twice on the fob and the truck starts. Now its when I press the start button again that the truck does not turn off. I all I get is a blinker flash when I press it once or if i press it twice a flash and honk, yet the truck remains running??? The issue has been driving me mad and cant find much on it. Any ideas would be greatly appreciated!

 

How close to the truck are you when trying to turn off. The following is from Ford.

Turning the Vehicle Off After Remote Starting

Press the button once to turn the vehicle off after remote starting. The parking lamps will turn off. To turn the vehicle off, you may have to be closer to the vehicle than when starting due to ground reflection and added noise from the running vehicle.

 

I have gone so far as to sit in the truck and try at this point..

 

Seems like you're doing it right for a 2013 (Ford dealer part number BC3Z19G364A, same as aftermarket kit FD1317009 for 2011-2014 F-150), but try this to shut off the engine:
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1. Press the remote start button on the remote control.
2. Within three seconds, press the button again.
3. The engine will turn off.