I recently crossed with this issue of having an extra entry automatically being added to my grub.cfg when I
sudo update-grub or
sudo update-grub2. Even when it is deleted and file is saved, it keeps on adding itself on the file and on the menu.
Here is the link to my grub.cfg for your reference http://pastebin.com/gDtUZs5N
Notice the lines 178-186, those are the extras what I am referring to.
I just to keep my grub menu as tidy as possible.