This problem occurs with Ubuntu Classic desktop not Ubuntu Classic (No Effects) desktop.
The windows bear some similarity to maximised windows under the new Unity desktop where the top border merges with the bar at the top of the screen. I can't stop this effect. Launching a new window causes it to appear at the top left of the screen with no top border so I can't move it to expose the window below.
I have read the post of a similar problem with a netbook under 10.10 where the culprit is a program called maximus. I have tried to find it in the list of processes by ps augx | grep maximus but it is not there; neither does it appear in the list of start up programs nor the list of current processes in the system monitor. So I guess it is not maximus that is causing the problem.