I have tried to fix this using the template options, and it removes the first home button on nav bar but the second on in the middle is still listed, and in the wrong place.

Here is a link.

see the options at ato->MENU 1 (Page Menu)

Are you talking about the menu option under "Appearance"? Thats the thing, it's disabled? I don't seem to have it as an option under appearances. Under page->menu bar if I set the "Home link in Page Menu Bar" to nothing it removes the first home button on nav.

That's correct, It removes the auto generated 'Home' link' you have probably created a page called 'Home' and have the 'Sorting order of Page Menu Bar' option set to 'menu_order'.

You need to go to each page and set the menu order so the pages will show up in the order you want. they are probably all the default value of '0'. Make one 10, one 20, one 30 etc