Okay, after enabling Single Public Zone, I then assumed the site directory was defunct and could be deleted. Replacing it fixes this issue.
SIDENOTE: Is there any reason (currently) not to have all content and modules in the root Welcome Zone. By default, we get two different start pages. Most people probably wouldn't want that by default. I would rather create a zone if I saw the need to, maybe even for Guest accessible content (but with the if_in_group tags and the options in the menu I think it's easy enough to work within the root zone). Just my opinion. Shifting everything into a zone just to allow for a public area at the root doesn't make sense in my mind. An admin could make a zone a public area easily enough if they felt the need, and dropping the site zone would simplify the breadcrumbs (and perhaps other things).
SIDENOTE: Is there any reason (currently) not to have all content and modules in the root Welcome Zone. By default, we get two different start pages. Most people probably wouldn't want that by default. I would rather create a zone if I saw the need to, maybe even for Guest accessible content (but with the if_in_group tags and the options in the menu I think it's easy enough to work within the root zone). Just my opinion. Shifting everything into a zone just to allow for a public area at the root doesn't make sense in my mind. An admin could make a zone a public area easily enough if they felt the need, and dropping the site zone would simplify the breadcrumbs (and perhaps other things).