Sort settings not staying after reboot

Sort settings are indeed not saved. That's not a bug, it's just not implemented. You can easily sort the items after a restart via Taskbar Inspector:

You can also configure a keyboard shortcut for even quicker sorting using advanced options, see:

https://tweaker.userecho.com/topics/885-sort-taskbar-items-automatically

Regarding "hidden items", what do you mean by that?

OK, I don't understand why keeping the layout the way the user set it isn't implemented. If you can right-click in the margin and select a sort option, why not make those options (or at least the popular ones) selectable as defaults in a config menu?

Where is this Taskbar Inspector? How is it easier to sort via that than via the menu itself?

Where are those advanced options for programming a mouse click to do the sort? I'll look at it, but again I don't see how that's any easier than right-clicking and sorting right in the menu. It's not that it's difficult to do, it's that it's annoying to have to go through the menus and do it on every one that gets messed up after a boot.

By "hidden items" I mean any menu item that you right-click on and select "hide". For example if you add a subdirectory as a menu item but don't want every subdirectory within it to be included in the menu, you just hide the ones you don't want. That's also something that should be saved in a config file to survive a restart.

I think that we're talking about different things. Which subdirectories are you talking about, what menus, what "hide"? Can you post a screenshot?