Unable to define app menu or set binds to open apps in WPrefs

[tragicCartoonist]

So when going thru WPrefs > Applications Menu Definition, anything I drag over does not save. I've gone through and manually added a program button in the menu.hook file, and that saves just fine. But, when I try to set a keybind for said program, it once again doesn't save. When I have ~/GNUstep/Defaults/WindowMaker open thru XFE's text editor and try to set the aforementioned program's bind, I get alerted:

/home/[user]/GNUstep/Defaults/WindowMaker was changed by another program. Reload this file from disk?

Whether I press Cancel or OK doesn't matter, there's no change, and the binds set in WPrefs still don't exist. I've ran WPrefs as root, changed multiple file perms to me r/w/e for all users, followed the syntax listed according to /usr/share/WindowMaker/menu, still nothing.

Edited to include more things I've tried to manually get binds working

[gryf]

Running wprefs as different user (including root) will cause to write configs as that particular user.

I've just tried with the fresh installation of Debian testing, and besides warning about menu.hook I have no issue with adding/removing items to the root menu. menu.hook in the menu actually prevents me from doing anything to the menu, so that I needed to remove the ~/GNUstep/WindowMaker/Defaults/WMRootMenu and say "Yes, discard and update" to be able to change the menu)