Comment 16 for bug 498995

Hello,

I encountered this bug also, but exactly as Pavel described it (Docky and Gnome-Do are on top, but all clicks pass through to the underlying app, with one exception: minimising all apps works - then Docky/Gnome-Do are receiving the clicks, so they don't go to the desktop then..).

Furthermore and really interesting: my bottom gnome panel is configured to auto-hide but additional those "go away" arrows are activated. Somewhen today I decided to toggle the gnome-panel to the right with this arrow ... and now I could not get it back since the arrow for the original gnome panel does pass the clicks through to the underlying app as well!
The top panel is not configured to auto-hide and it responded as usual.

This tip here solved it for me, at least currently: http://ubuntuforums.org/showthread.php?t=1274398

To sum up: Docky, Gnome-Do and gnome-panel on auto-hide behaved the same, always-on-top compiz rule solved it for now