After installing the Windows Logon Agent, all users are required to authenticate again when trying to log into their desktops while using Citrix. This double authentication still occurs even after uninstalling the Windows Logon Agent.
Citrix server uses its own gina.dll that supports chaining. This will allow a user to only need to authenticate once. Their credentials are passed to the user session on the desktop when they launch the session. This issue occurs because installing the Windows Logon Agent replaces the Citrix gina registry entry with our dll. When the agent is uninstalled, the registry key that we wrote is removed and hasn’t been replaced, causing the double authentication.
Restore the missing registry key so that the OS will load the Citrix dll. A restart will be needed and you will want to ensure that the correct Citrix gina.dll file still exists in the System32 folder prior to doing this.
The full steps to doing this are listed in this article on the Citrix website:
Windows Server 2003, SBS 2003