From a quick look this seems to be due to the fact that the spell plugin has path

/menu/Tools/ToolsOps_1/

while for instance docinfo has

/menu/Tools/ToolsOps_2/


maybe (just guessing!) when ToolOps_N with N > 1 a separator is always placed
above the item. In the tools menu this ends up in a separator at the top since
if the spell plugin is not active there are no items above the docinfo one.

This is a duplicate of bug #95733.

But since bug #95733 describes to different problems I'm going to move part of
bug #95733 here and change the summary in both the bug reports.

From bug #95733:

-----

Reporter: aes@gnome.org (Andrew Sobala)

When "Word count" (for example) is added to the tools menu via. the plugin
manager, there is a separator at the top of the menu.

------- Additional Comment #3 From Paolo Maggi  2002-12-10 04:45 -------

The second one is probably due to a libbonoboui bug: the "Wrod Count"
(now Document Statistics) menu item is added to a placeholder having
delimit="top" so the separator is automatically added by libbonoboui.
Probably, libbonoboui should add the separator only when there is at
least one visible menu item before.

------- Additional Comment #4 From Michael Meeks  2002-12-13 10:58 -------

[...] - if this irritates you enough we need a
libbonoboui patch to fix this - it sounds pretty tedious. One problem
though is that there is no way to notify an item 'below' that
something has been inserted above it. Of course for a placeholder's
contents its different. Ultimately that code was not particularly
designed for populating empty menus - hence it doesn't work so well :-)

fixed with UImanager switch