There are 2 different profiles in a fresh install - the unity & the default profile
The default profile by default doesn't have the Unity plugin enabled & uses the 'static application switcher', probably a few other diff.'s
At some point you may have switched to using the 'default' profile while logging into Ubuntu (unity-3d) & enabled unity, ect.
You may be able to set all back with a gconftool command but try this 1st. -
Login to Ubuntu (unity-3d) & then open this file
If it has this section in it then remove [general_ubuntu] & all below it, save. (or just remove all from the file & save as an empty file
Then open a terminal & run ccsm, it should show on line 5
Profile : unity
If so then your Ubuntu login is on the unity profile where it belongs
Then log out & in to Classic - start compiz if need be, then run ccsm from there. Line 5 should show
Profile : default
If so then any ccsm changes made in either Classic or Ubuntu logins will not affect the other login
The moment you click on "Preferences" in ccsm while in the Ubuntu session you will be switched from the 'unity' profile to the 'default' profile.
Sometimes this causes a hang, other times if you wait the desktop (control) will return, usually sans unity.
Here is a bug I have on this unfortunate occurence