Most of the time when I close the P2A Configuration Window some combination of "Respond To Radio" and "Change Frequencies" get selected weather I selected it or not.

Also sometimes "Respond To Radio" unchecks itself.

I'm running the most current stable release that I did a clean install on my removing any Pilot2ATC directories in "C:\Users\username\AppData\Roaming\ and re-installing from scratch.

You need to clear the Joystick/HotKey settings that toggle the copilot on/off.  They are just below the Co-pilot options check boxes.

Dave