Strange. Booting an Ubuntu LiveCD should not affect what's on the HDD.
Are you having to run Beryl Manager manually, or is the Beryl Manager icon appearing automatically in the top Panel?
If you click on 'Select Window Decorator' in the Beryl Manager pull-down menu, have you got 'Standard Beryl Decorator (Emerald)' selected? And have you deselected
'Launch Fall-back Window Manager if beryl crashes'? (If Beryl Manager is not already running, type beryl-manager in a Terminal window first.)
Also, there should be a file called beryl-manager.desktop in the directory /usr/share/autostart/