I have problems with Beryl (on arch linux though) in that if i start it from a session, i get decent borders/effects but not as many of the desktop transition effects (only left-right, no cube). However if i start beryl-manager i lose the borders, and get some rendering problems (rarely) but gain the mentioned cube like.
Beryl to me seems fairly unstable (although it's working alot better than XGL/Compiz).
One thing that seemed to help me was using the nvidia-xconfig to configure my xorg.conf
have you tried that?
- i used the Arch wiki, maybe some of the tips will help you