This happens in VLC, iTerm, Chrome, maybe others where a grey-ish bar appears where the menu bar would normally be and if I mouse over it the menu bar appears. In Chrome this sometimes appears when I have created a new window on my main screen, make it fullscreen, and move it to the second display, but if I exit full screen and re-enter full screen it works, but not for VLC or iTerm. Any ideas on how to fix this?
The third chrome image is what it looks like when it's working correctly (and the mouse is hovering to shown the menu bar).
Best Answer
If you don't care about it, you could remove the second menu bar in the settings. It should fix the problem.
http://www.mactrast.com/2013/10/disable-second-menu-bar-os-x-mavericks/