It is possible that when you don't use a prefix, that you have to make
symlinks from /usr/local to /usr (for example for the PanelApplet)
ln -s /usr/local/share/pixmaps/gcmapplet_small.png /usr/share/pixmaps/gcmapplet_small.png
ln -s /usr/local/share/pixmaps/gcmapplet.png /usr/share/pixmaps/gcmapplet.png
ln -s /usr/local/share/gnome-2.0/ui/GNOME_GcmApplet.xml /usr/share/gnome-2.0/ui/GNOME_GcmApplelibgtkhtml2_0-develt.xml
ln -s /usr/local/lib/bonobo/servers/GNOME_GcmApplet.server /usr/lib/bonobo/servers/GNOME_GcmApplet.server