I am not sure that the system uses NSUserDefaults for storage of these kinds of preferences, but it has the same behavior of toggling one setting changing many (as if reloading valid or invalid settings from a different source than when the list was initially rendered). The last time I went to make one when I double-clicked to add set the keyboard shortcut, all of my custom shortcuts were erased (unbound, but still listed).
I frequently make keyboard shortcuts to run small scripts running with Automator. the only thing I've seen like this on Mac is the preferences for custom keyboard shortcuts for Services within the Keyboard preference pane. I'm also seeing this bug still with 1.7.6 on macOS 10.12.4 (16E195).
