Hi,
If it is just a matter of icons in menus, you may look at the desktop file to see what name of icon is there and check if the same icon name exists either under /usr/share/icons or in /usr/share/pixmaps. After gnome icon theme was updated last time, some icons have stupidely changed their name, so that the desktop file calls for an icon name that will not answer anymore... see what I mean ?
Else, sometimes the icon needs to be in the other folder to be seen (in /usr/share/pixmaps instead of /usr/share/icons, or vice versa, not sure now). You can check that too.