When you enter the throttle cut function, you can set the level that the cut function moves to. There are two numbers you can set: Trigger and Cut. The trigger number is the throttle position that the throttle must be below in order for the cut to work. The Cut number is the position the throttle will move to when you activate the throttle cut.

If you have your idle endpoint set too low, then there's nowhere for the throttle to go to when you apply throttle cut. Normally, you want to have the throttle set up so that it's as mechanically as close as possible to proper movement, with only minimal adjustment of the endpoints to get it exactly set. Then, you have some 'room' for the throttle cut to work.