Comment 2 for bug 876999

Also affects me in the same way. Try this for a temporary workaround:

Log in to Ubuntu (3D) as normal. Open a window. Window is invisible.
Click on Workspace Switcher on the dock. The windows become visible again. Click on the workspace to use the window. (note that the title bar is still invisible if not maximised. If maximised, there will still be some minor problems. Using workspace switcher will fix most of these.

Now this is not a long-term workable solution, but it may help others work in the environment in question and be able to come up with a solution or a better workaround.