I had the same issue. It occurred when upgrading from DotNetNuke 04.05.05 to 04.06.00 using the source package. Here is how I fixed it.
Upgraded from 04.05.05 to 04.06.00.
I accessed the website and received the following error:
A critical error has occurred. Could not load the assembly 'DotNetNuke.Authentication.LiveID'. Make sure that it is compiled before accessing the page.
Copied the following files from the 04.06.00 install package (DotNetNuke_04.06.00_Source\Website\Install\Package) to the {website}\Install\Package directory:
LiveID_01.00.00_Install.zip
OpenID_01.00.00_Install.zip
Downloaded ActiveDirectory_01.00.00_Install.zip and added it to the {website}\Install\Package directory.
Via the browser, ran "http://{website}/Install/Install.aspx?mode=InstallResources" with the following results:
Install Resources Status Report
00:00:00.031 - Installing Package File ActiveDirectory_01.00.00_Install: Success
00:00:00.375 - Installing Package File LiveID_01.00.00_Install: Success
00:00:00.625 - Installing Package File OpenID_01.00.00_Install: Success
Installation Complete
Accessed the website and got the following error:
Parser Error Message: Could not load file or assembly 'DotNetNuke.Authentication.ActiveDirectory' or one of its dependencies. The system cannot find the file specified. (E:\Websites\DotNetNuke\Aqua-Marine\web.config line 68)
Copied the following files from the {website}\bin\Providers directory to the {website}\bin directory:
DotNetNuke.Authentication.ActiveDirectory.dll
DotNetNuke.Authentication.LiveID.dll
DotNetNuke.Authentication.OpenID.dll
Janrain.OpenId.dll
Logged into the website.
Under host setting, installed ActiveDirectory_01.00.00_Install.zip.
Upgraded from DotNetNuke 04.06.00 to 04.06.02 using the source package.
Upgraded from DotNetNuke 04.06.02 to 04.07.00 using the source package.
Upgraded from DotNetNuke 04.07.00 to 04.08.00 using the source package.
Everything seems to be working OK. Hope this helps.