Reporting bug as advised by brainstorm moderators, http://brainstorm.ubuntu.com/idea/27775/
The menu bar that appears when hovering with the mouse over the top panel is aligned the same for both maximized and non-maximized windows. In the case of maximized windows, the alignment allows for the close, minimize and restore buttons to fit between the Ubuntu logo and the menu. In the case of windows that are not maximized, the space where the buttons would be is unused, and the window title is faded out when the menu is overlaid on top. I think this looks unclean and the menu should use a different alignment for non-maximized windows.
The most straight-forward thing to do is, I believe, to align the menu to the left for non-maximized windows (immediately to the right of the Ubuntu logo), thus completely obscuring the window title.