Comment 4 for bug 159217

Obviously the problem is with the autostart order of gnome. When the startup of awn is delayed then the icons are popping up in the middle like they should. Maybe there is some compiz-stuff which needs to be loaded before awn for the visual effects.

Workaround
----------------
Start awn via the following bash:

#!/bin/bash
sleep 3s
avant-window-navigator

Just save it as sh-file somewhere on your hd, and put it in your autostart.