Desktop: Xfce 4.12.3 Distro: MX-18_x64 Continuum Dec 20 2018 base: Debian GNU/Linux 9 (stretch) If "Show menu hierarchy" is enabled in Whisker Menu's configuration the "Settings" category is moved to the top of the list of categories in the menu, just under "All". Resetting the panel to its default settings restores it to just above "System" but within a short time it's been migrated back to the top. No other categories are affected, only "Settings". Unselecting this option stops "Settings" from migrating. This has been confirmed by other MX users in its support forum. Once "Settings" has been moved within Whisker, the Xfce Applications Menu also shows Settings as the first category (followed by Applications, Development, Games, etc,) even after "Show menu hierarchy" has been disabled in Whisker. If Applications Menu has been used all along, never Whisker, the Settings category stays put. Note that MX doesn't have subcategories in its menu. Can be reproduced at will by enabling/disabling the menu hierarchy option in Whisker.
This is expected behavior. By default, Whisker Menu sorts the categories and items. However, when you turn on "Show menu hierarchy", it instead uses the order defined in the menu file for both categories and items. No sorting involved. The default Xfce menu file puts "Settings" at the top, so it goes at the top. The Xfce applications menu always follows the order defined in the menu file for categories and items. With "Show menu hierarchy" turned on, they follow the same order for items and categories. I have never seen "Settings" anywhere but at the top in the Xfce applications menu. Whisker Menu cannot influence it; they use different settings files, run in different processes, and do not use IPC. Changing a setting in Whisker Menu will not impact the Xfce applications menu.