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Most Strange IIS Windows Authentication behavior?

I had this same problem on my Windows 2008 R2 server. I did not have custom 401 error pages. I did use aliased server names (via DNS CNAME records and host header entries on the IIS bindings). I registered the SPNs for Kerberos as suggested, but that did not solve the problem. I resolved it by disabling "Kernel Mode Authentication" (click on the server in the IIS tree -> double-click on Authentication under the IIS group -> click on Windows Authentication -> click on Advanced Settings on the Actions pane -> Uncheck the checkbox -> click OK -> run iisreset). The information on that dialog box recommends against disabling Kernel Mode Authentication when using non-standard service accounts for the application pool identity, but that didn't apply to us since we're using the standard ApplicationPoolIdentity identity.