I'm experiencing this problem on a couple of sites with FEE. When it is activated and I'm logged in the front end appears like this:
My website is here: http://siobhanmckeown.com (though you can only see issue when logged in.
I thought this was a theme issue but I've installed FEE on a client site and am having the same problems. When I deactivate the plugin this disappears.
I can deal with it personally, but I can forsee confused clients. Is there any way around it?