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I think you need to check with Microsoft
If i search i get the following as part for SCOM: http://support.microsoft.com/kb/975931 and for SCCM this forum topic; http://social.technet.microsoft.com/forums/en-US/configmgrgeneral/thread/e985a41 3-60bf-47c6-988a-716ddb38af4c/
mind that for SCCM you need to check the ITMU exclusions aswell since these are not part of SCCM but used by it for product patching
I would strongly suggest logging a case for this so we can establish which exclusions are vital. Excluding entire directories poses substantial risks and should be avoided where possible. Your log files should also indictate which executables are the issue.