that is because you when you set ato->Page Menu Bar->Border around all menu items to 'solid 1px #000000', it puts a border around the menu area and a border around each menu item so you are seeing a 2px border on that side. If you want to get rid of it add the following to the ato->Add HTML/CSS Inserts->CSS Inserts
HTML Code:
div#menu1 ul.rMenu {
background: #FFFFFF;
border-left: solid 0px #000000;
}