When you installed the manager, did you use the default website or did you specify to create your own?
There are many threads to this subject of boh WSUS and SEPM living side by side.
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Description:
Symantec Endpoint Protection Manager and Windows Server Update Service (WSUS) can not be installed on the same website. In certain situations, WSUS will utilize the IIS default website. In this case, installing the Symantec Endpoint Protection Manager on the same machine may therefore cause issues. This occurs since WSUS (if using the default website) creates a Virtual Directory called Content. The Symantec Endpoint Protection Manager installation thus also creates a Virtual Directory of the exact same name and overwrites the WSUS directory (since both use a virtual directory called "Content." This directory can be overwritten when installing either application on the same website.
Resolution:
Before installing Symantec Endpoint Protection on a computer running WSUS, check whether WSUS is installed on a default web site. If WSUS is running on the default website, choose a custom website in the Symantec
Endpoint Protection Management installation wizard. If WSUS is running on a custom website, choose the default website. If installing WSUS on a computer running Symantec Endpoint Protection Manager utilizing the default website, choose custom website in the WSUS installation wizard.
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Taken from:
http://www.symantec.com/support/endpointsecurity/customer_installations_issues_with_resolutions_int_112007_partner.pdf
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Also, one might consider upgrading to SEPM 12.1
Because 12.1 now uses Apache and WSUS IIS, there will no longer be the same conflicts over the IIS website and port information.
Of course, it is stil recommended to use a "custom port" for installation of SEPM on the same server as WSUS.