In Ubuntu 11.04 with unity 3.8.16-0ubuntu1~natty1 when clicking an indicator its icon turns opaque and the menu shown is also opaque, regardless of the panel opacity value. I think both the icon when clicked and the menu should follow the value set by Panel Opacity in CCSM. Is this a valid bug?
It is somewhat of a valid bug, except that the menus are controlled by a separate plugin. To make menus transparent (to some extent) use the following values: