Ah, that would explain it, one of the accounts is a site admin, but you have logged in with the other (who is not a site admin), so now all the Atlassian stuff thinks you are the unprivileged one.
I'm afraid there's no easy way to work with two accounts at the same time yet (it's a very popular request). I usually do it by firing up a different browser, or the "privacy mode" version of my main one.
Site admin gives you the ability to admin the site, but not necessarily automatically all the applications within the site. Equally, Admin on an application may not be tied in with site/person admin.
Could you give us the url you land on when you click the users tab in admin? (Obscure your site name if it's in there, we don't need that bit)
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