I've posted a beta of the 01.00.04.36979 release of the provider here.

RELEASE NOTES:

This is the third release of the Active Directory Authentication Provider since being separated from the DNN Core code.

The provider requires Full Trust in order to operate.

If you currently have a 01.00.04 beta version installed you'll have to either uninstall it and install this version or after you install this version you'll have to manually copy the .dll into your bin\Providers folder (the package installer doesn't copy the .dll if the version is the same in the .dnn file).

Changes/Fixes for this release:
Same as in this post (http://www.dotnetnuke.com/Community/Forums/tabid/795/forumid/89/postid/218593/scope/posts/Default.aspx)
Plus:
ACD-7422 - Role Synchronization Not Working On W2K Domain Controllers
ACD-7532 - Typo in pop up help for email domain on windows auth provider config screen
ACD-7664 - Auto Login IP Addresses
ACD-7488 - ActiveDirectory redirects web service files to the WindowsSignin.aspx file.

The fix for ACD-7422 resulted in a whole different way of searching the AD for groups and it should be much faster and cleaner than the way I was doing it before. There shouldn't be a reason for any timeouts using the new code.

I've locked the other beta post so if you had a question that was in there that I haven't answered ping me in this thread.

Thanks Briana. I don't have the core packaging code in front of me but it looks like it's failing either when it tries to make a backup of your current web.config or when it's trying to make the necessary changes to it. I'm wondering if the file was perhaps locked from the previous uninstall (though I don't recall ever seeing that) or perhaps the permissions changed on your web.config file. What previous version did you have installed? Can you install that version again?

Check your bin/Providers directory and look for any instances of the DotNetNuke.Authentication.ActiveDirectory.dll. If there are then delete them. Then check under DesktopModules/AuthenticationServices and see if there's an ActiveDirectory directory. If there is then delete it. I'm wondering if perhaps an uninstall didn't go right and it left files behind. I don't have access to the database right now or I'd give you same tables to check in there as well. Once I can I'll do some checking there as well.

The .dnn manifest files haven't chaned over the versions except for updating the version # and to remove a .dll that I was using before the latest 1.0.4 release so it's not making sense that one version fails at a later time than another. 

EDIT: Got access to one of my databases. Check the Authentication and Packages tables and make sure there's nothing ActiveDirectory Related in those tables either.