The Unity launcher on my system has display issues, all the icons are scrunched up under the menu bar. I've restarted my machine, logged into the GNOME session and back into unity, and triple checked the settings in CCSM, but it just stays broken.
It appears to be a display issue, if I right click on the "unused" grey parts of the launcher bar it brings up the context menu for the applications in the correct places, but it just refuses to display them anywhere but mostly hidden under the menu bar.
This is obviously quite irritating. ;)
Here's a screenshot demonstrating the problem: