How do you tell unity to startup in 2d and compatibility mode? If you have to run a UNITY --replace after startup it doesn't kill the currently running unity and you end-up with two toolbars. One superimposed over the other. I would assume the best way to fix this is to have unity 2d start off in compatibility mode right off the bat.
SnapOverflow
Can't you simply choose Unity2d in the login screen, then log in? It should remember your last choice automatically.
Log out from your current session. Then, in the drop-down menu next to the password prompt, choose "Unity2d". Log in again and you should have the desktop you want. The next time it should log you in to that by default.
You did not make mention of what version you are running so....
How to configure 2D http://ubuntuforums.org/showthread.php?t=1748671
Another installation guide http://www.linoob.com/2011/04/unity-2d-on-ubuntu/
If you have Ubuntu 11.10 or later installed you should be able to log into unity 2D easily enough.
You might log into Ubuntu in failsafe graphics mode, then activated proprietary video driver. You activate driver by going into system settings > Hardware > additional drivers.