black background behind all buttons on toolbar containing address bar:
in skin.ini, specify a color:

[Addressbar Skin] 
Color = #dddddd

weird bar at the top with caption buttons and the opera menu, even though you
had the opera menu somewhere else:
The "show close button on tabs" setting is broken as of Opera 12, and forces
this weird caption bar to appear. You can still disable the tab close buttons
(which are completely unnecessary, as you can middle-click to close a tab), by
enabling tab close buttons but doing this in skin.ini:

[Pagebar Close Button Skin]
width = 0
height = 0