I just found out that I have lots of duplicate keyboard shortcuts for the same functionality. Don't know how they got there, but I cannot clean them up, delete options are greyed out. See the screenshot. Checking/unchecking their checkboxes or clicking on the "Cancel" menu item doesn't have any effect on the greyed state of the delete controls. How do I clean up this mess?
Those are hotkeys assigned to buttons and menu items on your toolbars.
It looks like you have more than one copy of the Menu toolbar, for example. ("Menu" and "Menu (1)".)
You can remove the hotkeys from the toolbar items if you want the items but not their hotkeys. Or you can remove the items entirely, or remove the toolbars if you aren't using them.
The hotkeys list tells you which toolbar each item is coming from, in the "Toolbar" column.
The same dialog has a Toolbars tab at the top. Look there are well. You may have toolbars which are not visible, but which have "always enable this toolbar's keys in listers" turned on. (This is there mainly for the Menu toolbar, because people would turn it off and then complain that the standard hotkeys inside it, like Ctrl-C/Ctrl-V for copy and paste, stopped working. But if you make a duplicate copy of that toolbar, you'll only want the hotkeys from your copy and not from the original.)
The "always enable ..." checkbox did the trick. I would like to delete the original Menu toolbar, as I'm not using it, but I guess allowing that would to much of a risk for users not knowing all the details, myself included .