I might be missing something, but this happened with me in Sharepoint too. It was maddening. In fact, even when I gave user permissions to a site, if I logged in as that user, I couldn't even SEARCH for the site. I had to use the actual site address and then star it as a favorite. Then it would show up on the user's Sharepoint main page.

Microsoft has been doing a lot of things right in recent years, but they still do a lot of stupid things.