In the past, I've run into this problem when scripts register using the deprecated form where the menu path is specified in the 'script-fu-register' procedure, rather than using a separate 'script-fu-menu-register'.
For example, instead of doing
(script-fu-register "script-fu-rectangle-path"
_"<Image>/Script-Fu/Shape Paths/_Rectangle..."
"Creates a rectangular path."
:
:
:
)
Scripts should now be registered with a call to both script-fu-register (specifying the command name):
(script-fu-register "script-fu-rectangle-path"
_"_Rectangle..."
"Creates a rectangular path."
:
:
:
)
and a call to 'script-fu-menu-register' (specifying the menu location):
(script-fu-menu-register "script-fu-rectangle-path"
_"<Image>/Script-Fu/Shape Paths" )