I also had the experience of Gnome's Visual Effects reverting to "none" each time I logged out. But it turned out to be not so much a bug as a case of non-obvious UI design. I got what I wanted as follows:
1. Log in to a Gnome session
2. Go to System > Preferences > Appearance > Visual Effects
3. Select "Extra"
4. Click "Close"
5. Go to System > Preferences > Startup Applications > Options
6. Click "Remember Currently Running Application"
This gives a notice that the session has been saved. Then I configured Compiz the way I wanted it and logged off. Next time I logged on Compiz was running by default and my settings were preserved.
I also had the experience of Gnome's Visual Effects reverting to "none" each time I logged out. But it turned out to be not so much a bug as a case of non-obvious UI design. I got what I wanted as follows:
1. Log in to a Gnome session
2. Go to System > Preferences > Appearance > Visual Effects
3. Select "Extra"
4. Click "Close"
5. Go to System > Preferences > Startup Applications > Options
6. Click "Remember Currently Running Application"
This gives a notice that the session has been saved. Then I configured Compiz the way I wanted it and logged off. Next time I logged on Compiz was running by default and my settings were preserved.