I just noticed this today and I cannot understand why this is happening. So I set the System Preferences > General > Appearance to Graphite (The Traffic Light I cannot stand). Everything was fine. About 10 mins ago iTunes, and only iTunes was doing the invert of what was chosen in System Preferences. Now, two of the three buttons do the invert of the correct colors. IE it will be red, yellow, grey or grey, grey, green. I did a PRAM reset and same issue. Any idea what this could be or how to fix it?