When I first answered your question it was because I saw we have logic to create a user
if (Context.User.Identity.AuthenticationType == "NTLM" )
at that time I changed it to this:
if (( Context.User.Identity.AuthenticationType == "NTLM" )|| ( Context.User.Identity.AuthenticationType == "Windows" ))
So if you have the newest version of mojoPortal I think it "should" automatically create a mojo user for windows users in the application_AuthenticateRequest event in global.asax.cs
Hope it helps,
Joe