When I go to Menus the top-level ones listed are Dashboard, Top Navigation, User Navigation, Security, System, and Support. All but Security and System I see in my menus. Even if I add the needed permissions indicated to enable System (menu_system) and the one item under it (manage_workspaces), it does not show up anywhere in my menus. Same thing for Security. I imagine these two must be left over from 2.2.N, from which I've upgraded just about all my sites. So, shouldn't the 2.3 and 2.4 installers get rid of these old menus, since there is nothing to make them show up now? It's just confusing to have them in there if they do nothing.
Gotcha! I didn't encounter this issue when upgrading from previous runs, but that's probably irrelevant. I mentioned the cache folder, because MODX does indeed cache menu items. See: core/cache/menu/menus. Depending on folder permissions, some stuff may or may not be cleaned up during upgrades.
A MODx Fanatic
I think they are a hangover from < 2.3 because there are still user permissions that refer to those menus too.
I think the gear icon is the "System" menu and the Access Control Lists entry under that is the "Security" menu.. I could be wrong.
That's what I thought initially, too. But, it seems that's called "About" in the menu system, and it's the third item under the User Navigation heading. I've gone ahead and deleted all these extra menus, with no effect whatsoever on what shows up in the menus. I looked at an older website using 2.2.16, and indeed there was a "Security" menu there, as well as "System" and other stuff. It's weird that the other menus that were in 2.2.X were deleted when upgrading to 2.4, but I suppose they were just given new parents rather than getting deleted.
It's weird. 'Access Control Lists' appears twice (among other things). It looks like you're right that there's some leftover stuff from earlier versions.