If your using Warthog Throttle w/ TARGET SE (Thrustmaster TARGET Script Editor), and want to use the AP Select Switch or any other 3 way toggle, you need to remove any "PULSE +" modifiers for those switches.
Try this:
//Autopilot Select Switch *************************
MapKey(&Throttle,APPAT, DX1);
MapKeyR(&Throttle,APPAT, DX2);
MapKeyR(&Throttle,APALT, DX2);
MapKey(&Throttle,APALT, DX3);
These commands need to be made with DX button pushes. If you use keyboard commands you will get conflicts and sticky keys, because the toggle switch, without the "PULSE +" modifier, will send a continuous key press to the system.