Comment 2 for bug 374850

Issue was fixed by adding icon_name = name on line 259, like so:

...
252 elif name+".desktop" in self.apps_by_id:
253 icon = self.apps_by_id[name+".desktop"].get_icon()
254 if icon.__class__ == gio.FileIcon:
255 if icon.get_file().query_exists(None):
256 pixbuf = self.icon_from_file_name(icon.get_file().get_path(), size)
257 if pixbuf != None:
258 return pixbuf
259+ icon_name = name
260 elif icon.__class__ == gio.ThemedIcon:
...

All icons, including my Eclipse, are now visible.