I just upgraded from 12.10 to 13.04 and I'm having trouble getting the Cairo-Dock theme on my system working. I upgraded on the Cairo-Dock theme (if that makes a difference) and it was just the Cairo-Dock, with no Ubuntu side and top bar. Now, as you can see in my screenshot:
both Ubuntu and Cairo docks are showing. And before you ask, no I'm not using the default Ubuntu theme. Thanks in advance for the help!