Please check out the image below, there are four sites listed on the right side but only three of them appear on the drop down menu on the left. The site that is missing is not the main website.
This is because you're only a member of 3 sites. As a super admin you have the ability to view the full site list via the network admin, but that doesn't mean you're a part of every site.
The admin bar menu only lists the sites you're a member of, not the full list, that's how it's intended to work. Otherwise users would see sites listed that they have no access to.
For example, on my own site, there's a subsite I created for a friend. It does not appear in the admin bar menu either. If I look at the users page, I am not listed.
The only reason I have access is because I am a super admin. As a result it's listed in the network admin, and I can access the site as if I were an administrator.
Despite my super admin access, until I add myself to the site I won't have a role on it, and it won't show in the admin menu.