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Windows SharePoint Services and SharePoint Portal Server do some nasty things to a virtual server. Things that will cause ASP.NET application such as Directory Update to not work. We recommend that Directory Update NOT be installed on the same machine as SharePoint. Ideally, we recommend installing IIS Web Services on one of your domain controllers and using that machine as your Directory Update machine, but that is not always possible due to an organization's security policy, web server management policies, SSL certificate availability, etc...
It is possible to tweak SharePoint enough to allow it to coexist with Directory Update. We tested this in the following environment: Windows 2003 SP1 Active Directory Windows 2003 SP1 member server SharePoint Portal Server 2003 SP2 SQL Server 2000 with SP4 v1.0.0 release of Directory Update Integration of Directory Update on an existing is a little tricky because of the fact that when you install SharePoint Portal Server on a Windows 2003 machine, it makes quite a few changes to IIS and the default applications.
First, locate Microsoft KB article 828810 “How to Enable an ASP.NET application to run on a SharePoint Virtual Server” since you will need those instructions plus some text that you will need to “cut and paste” in to the c:\inetpub\wwwroot\directoryupdate\web.config file. Confirm that ASP.NET is included (checked) in Control Panel -> Add/Remove Programs -> Add/Remove Windows Components -> Application Server Details.
Install the Directory Update application on an existing system Using the SharePoint Central Administration web page and the steps in KB 828810, exclude the /directoryupdate virtual directory Using IISAdmin, make sure that Integrated Windows Authentication and Anonymous authentication are enabled for the /directoryupdate virtual directory (found on the Directory Security property page – click the Edit Authentication and Access Control settings. Using IISAdmin, on the Directory property page, change the Application Pool to the Default Application Pool. Using IISAdmin, confirm that on the Documents page that the default.aspx is the default content page.
For the web.config file found in the C:\inetpub\wwwroot\directoryupdate folder, perform steps 1 through 5 At the command prompt on the server, run IISRESET (This WILL kick off any users on Sharepoint or any other web sites while it resets!) Try to connect to the http://localhost/directoryupdate URL and then logon as a user account.