Installed a Visual Basic web app on a Windows Server 2003 box with IIS 6 today and got some strange intermittent symptoms. The customer could login about 2 times out of 3, and could access some second-level pages intermittently, but other second-level pages would fail immediately. Failures took the user back to the login page.
The Event Viewer showed an error each time the user got bumped back to the login page, saying "Registry Key for IIS subauthenticator is not configured correctly"
I found the Microsoft KB article with instructions to enable IIS management of the anonymous user password. After applying the 3 steps the website works perfectly.
Took a while to resolve because I was baffled by the intermittent nature of the error, but once the correlation to the Event Viewer error was observed it was quick.