UPDATE:
hi guys, i had an intuition: i went to check the file /usr/share/WindowMaker/appareance.menu and i found this:
#include "wmmacros"
Appearance MENU
"Background" OPEN_MENU background.menu
"Styles" OPEN_MENU -noext STYLES_DIR USER_STYLES_DIR WITH setstyle
"
Themes" OPEN_MENU -noext THEMES_DIR USER_THEMES_DIR WITH setstyle
"Icon Sets" OPEN_MENU -noext ICON_SETS_DIR USER_ICON_SETS_DIR WITH seticons
"Save IconSet" EXEC geticonset USER_ICON_SETS_DIR/"%a(IconSet name)"
"Save Theme" EXEC getstyle -p "%a(Theme name)"
"Preferences Utility" EXEC /usr/share/GNUstep/Applications/WPrefs.app/WPrefs
Appearance END
so I stripped away all items with USER_*, and now my menu no longer has the annoying double items I described; I still have to work on the Background/Images submenu but now I think I figured out how to do it
stay tuned ;)