You could try looking at the choke plate when the choke is turned off. If it's not 90 degrees to the carb body that would cause the engine to run rich and rough, even rough enough to stop the engine from starting. Also if this has not been touch on; the main reason for the using an alternate method to turn off your engine other than the programmed throttle kill is so that if anything would happen to your throttle servo or channel in flight (Strip thottle servo gears, servo breaks loose from mount, or any number of things that can interfere with the throttle) it can be remotely shut down.
Believe it or not this has happend numerous times at the fields I fly at, Mostly with glow but the times that it happened on a gasser it was really dangerous because the servo seems to always stop or get stuck at a high idle position. Know the plane is to fast to Land safely and the engine is running to slow to burn out the tank. Imagine flying for hours not being able to do anything but creep around the field at a gliders pace. This happened to 2 friends and they both lost there new planes after there transmitters died out.

I use the programmed throttle kill as my primary and the choke servo as a backup. I like to start the engine without reaching inside the cowl but I think the electronic kills are the best. This eliminates human error and servo failures, and for there cost compared to the cost of these planes it's should not even be and issue