I searched the forums and found lots of complaints but these don't seem to be the same problem (or maybe they share a common cause).

I have two graphic apps which have poor performance in Unity 3D but perform well in Unity 2D and Classic. What I think I see: a time delay between the program writing to the window and the actual visible window update. This is something like half a second. The result is jerky motion inside the window. There is no significant CPU load during the time delay. In some cases the entire desktop locks up for several seconds. There is nothing wrong with the functionality - only the time delays and jerky movements.

I tried playing with the compiz settings (as some other threads suggested) but found no significant change.

I have an Nvidia GTS450, a mid-range card. As I said, this card performs well with Unity 2D and Classic.