Ubuntu 11.10 is out and filled with GNOME 3 featuring the gorgeous Unity 3D shell (by default) and an optimized panel, Unity panel.
Unity panel introduced a new placement for indicator, new transparent buttons when the Dash is active but the "alien" themes are not quite integrated in term of Unity panel which display fallback buttons when the window is in fullscreen mode.
This can be easily fixed for most of the GTK+3 themes via few easy steps (this "demo" provides the adjustments for Zukitwo):