Kinda hard to describe. But went back to try Unity mode and an issue that existed in 6 is still there. When I bring an applicaiton window up (click on it in the dock) and it is over another application window, If I click the window focused it goes to the back and the window below shows.
So for example :
SmartGit is open, I then open Chrome (it is now in focus). I then click on Chrome to use and it disappears and SmartGit is focused and clickable. Chrome has now moved behind as if I switched windows.
Now when I went into Unity yesterday this did not happen. This morning coming out of sleep the issue arose. Could be concidence, not sure. This is happens under Mavericks and Yosemite.
Kevin