I’m not having any problems saving either hotkeys assigned to K or N, or a custom menu assigned to those keys, and having it persist after a restart.
There may be an issue with the custom menu itself, or some function you have assigned to it. Are you able to assign this menu to any key and have it persist after a startup? We may need to take a closer look at that menu.
Likewise, are you able to assign any other function to those keys, and have it persist? Something simple like Polyframe mode? There may also be some aspect to your installation environment that is causing a problem.
Here is a video illustrating the creation of a custom menu, and the assignment to a hotkey.
If the video doesnt help you resolve your issue, you will need to contact Pixologic Support for us to take a closer look at your problem.