I am getting duplicate users depending on how they log in. If a user is logged in via auto login, a user account is automatically created in the form of domainname/user. Then if that user logs off and logs back in that user name will not work, they have to log in using their email user@domain.com which causes DNN to create a new user account. The result is that two usernames are created in DNN for the same user one in the form of domainname/user and one in the form of user@domainname.com; they both have the same access. i.e the Blog module recognizes both users as the same and gives them access to the same blog content.

The other problem is that now my users have to select the windows login button in order to use their AD username and pass. In previous versions there was only one login box and it worked the same for both AD and regular users. This is a problem because most of my users have no idea what the difference between windows login and normal login is.

Are your users trying to login as domain\user or just user? They have to enter their credentials as domain\user as that's how it's stored in the database though I've used this script (http://www.dotnetnuke.com/Community/ForumsDotNetNuke/tabid/795/forumid/89/threadid/60815/scope/posts/Default.aspx) on our school's site so that our users don't have to enter the domain name.

As for two accounts getting created......that's a known issue and I haven't decided on how best to handle it as some admins would want the accounts one way and others the other way.

The separate buttons are a result of the authentication providers being separated out of the core. If you had the other providers enabled you'd see buttons for each of them as well. Is your site just for AD users or do you have users that don't belong to the Active Directory? If they're all AD users then you can disable the DNN standard login and only the Windows Signin will show up (you'll want to promote your AD account to Admin or Host status first). If it's a mix of users then, unfortunately, the answer is to educate your users on the difference between the logins.

I have a feeling that the reason they cannot log in with domainname/username is because the password is autogenerated for autologin users.  I could be wrong but i think thats what i read somewhere.