Pasted from a reply to a review:
The issue has nothing to do with us or our code. WP only allows one plugin to hook in to the Nav menu editor.
Another plugin developer created a solution years ago that lets multiple plugins work there at the same time. But all plugins must use that method or what you are seeing happens.
We have used that method since v1 so there is nothing we can do there honestly. Can you disable our stuff there likely yes, but that would be custom code completely unique to your site to deactivate our plugin on only the right menu ids.
Better solution is having your other plugin fixed to be compatible with every other plugin on the repository. That solution and complete info on the problem is available here: https://docs.wppopupmaker.com/article/297-popup-maker-is-overwriting-my-menu-editor-functions-how-can-i-fix-this
That is from another of my plugins but it’s the same issue.
This was posted by the developer as a response to a review. The explanation makes sense from my knowledge of wordpress.