So you can login when it goes to the login page? Is this happening after you are logged in?

The only reason you should be getting directed to a login prompt is if the page is secure and you are not in the role that is required. 
If you are creating your own links then you need to make sure that the link has a tabid or a parent id on it or you will get logged out.

Can you post a link to the real site, I may be able to tell by looking at the page output.  
If you don't want to post it then you can e-mail it to me (click on my profile link for e-mail).

Thanks for your help John. I tried changing the settings back to unspecified in the admin site settings and left it alone for a few days. The home page is now working fine and the root links are as well. It's still a little strange that initially the home page comes up blank, but if I link directly to the tab then everything's OK. I'm using an HTML splash page outside of DNN to link into the DNN store, so it's not an issue. Good enough for now!