Business Objects SSO displays incorrectly

I am in the middle of setting of Business Objects SSO to automatically sign in using the tomcat connector. We can successfully logon using our AD when we go to server:8080/InfoViewApp/logon.jsp with no display issue but when we log to server/InfoViewApp/logon.jsp it successfully logs us in but shows the entire Business Object window inside of the center of the Logon Screen window.
Not sure where the error is since it looks fine when we bypass the auto login connector by going straight to 8080 and by passing IIS. I attached a screenshot of the misshown window.
http://y-wing.net:8080/bobj.jpg

I'm not sure why you would use trusted auth IIS when we have AD SSO built into tomcat offering a much more secure, better performance, and all round more stable choice that is 100% supported by SAP. If it's because your CMS's are on unix we have written another solution to setup SSO with tomcat only in Kb KB 1537480 (as the configuration changed slightly in SP3 this document should only be used for XI 3,1 SP3) It can be applied to earlier versions to 3.1 by changing the vintela steps and possibly that url.
Regards,
Tim

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