It's possible that the unity plugin isn't enabled anymore, so you need to check & enable it if it isn't
This needs to be done while in the ubuntu (unity 3d) session, there are numerous ways to do this, picking one -
Log in to ubuntu and go Ctrl+Alt+t on the keyboard, if a terminal opens great.
If a terminal doesn't open, then up in that top panel click on "Go". In the nautilus window, on left side in Computer section click File System & then browse to usr > share > applications. Scroll down & d. click on the terminal icon
If you don't know if compiz-config-settings-manager is installed then run this in the terminal
sudo apt-get install compiz-config-settings-manager
Once it's installed or if it already was then run this
scroll down & enable the unity plugin if it isn't enabled
P:S.: If CCSM is installed, it works in Unity 2D sessions as well.