This problem does not exist on Mac. It was found on Linux (otf2) during R8 It2 hackathon 2012/11/14.
1) Open at two MCT windows. Arrange them so one is partially obscured by the other.
2) In the window that is on top, use the Windows menu to choose another window to surface. Note that the chosen window does not surface despite its window title bar changing color to indicate that it now is the active window.
Duplicate of #32