I had the same issue and just found the problem. When I blanked out ATO --> Menu 1 (Page Menu) --> Home Link in Page Menu Bar, to omit the extra "Home" link, I inadvertently put a space in there, causing a blank <span> to be displayed in the menu bar. I finally went back and made sure I hit the delete or backspace key to make sure there were no spaces in there, and it got rid of it.
Just wanted to post this, so that someone else with this problem can try this solution, since I didn't find it elsewhere.
I tried to post it on "How to remove extra 'Home' page in the menu", http://forum.bytesforall.com/showthr...page+menu+item
, but I couldn't. It might be helpful to warn those doing that about not putting a space in there.