Implementing AD Authentication and have it work properly on a DNN site has a few steps to it. We spent some time getting this to work so we decided to compile all the steps into one article.
Step 1 - Install and configure the AD Authentication module.
The next two steps change which login tab is on top and what a user sees first.
Step 2 - You will need to edit the SQL database. Open the Authentication table. You will see two entries - DNN and AD. Make sure the ProgramID for DNN is higher than the ProgramID for AD.
Step 3 - Edit the Login.ascx file (\DesktopModules\Admin\Authentication). Look for the DNNTabStrip control. At the end put SelectedIndex="1". This puts the focus on the Windows tab not the DNN tab.
Step 5 - Create a new login page on your web site with the Account Login module on it. You do not need to show it in the menu but you do need to make sure All Users has permission to view the page. Then assign the new skin template you created in step 4 to it.
Step 6 - Lastly you need to change the default login page. Go into Admin - Site Settings. Then on the Advanced Settings tab change the Login page to the new page you just created.
Log out of the site and give it a try.