I see this behavior from time to time where a site’s URL will be in all capital letters when linked from the navigation. The site’s name is not all caps, and the URL is properly cased in most situations. The all uppercase treatment appears to come and go, and is not related to anything. Has anyone else seen it or know how to stop it from happening?
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I’ve just looked into this myself. It’s part of the internal caching; sharepoint converts part of the links to uppercase to make the comparison case insensitive. As far as I can tell there’s nothing you can do about it.
http://support.microsoft.com/kb/953457