Thanks for your feedback. I was actually aware of this, but I thought I’d made a fix for it. Right now, the capabilities are edit_theme_options which is in the same “scope” as activate_plugin, so switching between them should not change anything, but I will look in to it and get back.
Can I also add my voice here.
I seem to have the same problem:
I have users that have editor capabilities. I am using Admin Menu Editor Pro to provide an essentials view for editors and below. Even though the Sidebars menu is turned off for those users, it still appears but with ‘Categories, Tagas, News Categories, Resource Categories’ [the later two being custom taxonomies]. Happy to provide a clone on a testing site if it will help solve this.