Upon installation of Xubuntu from the daily-live image created on Jan 29, 2011 the program Gnumeric presents itself with two menu entries. One is in the Office category and one is in the Science category. The version is Gnumeric 1.10.2-ubuntu2 if that helps. This double entry is not present without Xfce4.8 installed.
Mmmh, I'm not sure it's a bug in garcon after all. Quoting the spec (http://standards.freedesktop.org/menu-spec/menu-spec-latest.html): Desktop entries should list all categories that clearly apply. They should not list categories that only vaguely or possibly apply, because the user will end up seeing the same desktop entry in a half-dozen places. But it's typical that several categories will apply to a given desktop entry. So I think garcon behaves correctly. I think what you want can be achieved using a few <OnlyUnallocated/> (cf. http://standards.freedesktop.org/menu-spec/menu-spec-latest.html#menu-file-format).
Yep, I double checked, the spec is like that.