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
gedit ~/.config/compiz-1/compizconfig/config
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
[general_ubuntu]
profile =
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
Edit:
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
https://bugs.launchpad.net/ubuntu/+source/compizconfig-settings-manager/+bug/880679