Update on issues from last week:

We continue to get reports of failed updates, slow logins, SCEP scans failing, and application crashes. It seems likely at this point that all of those issues are related to the bad SCEP update.

Base team are trying the hotfix on some affected machines now. See parent ticket for updates: 0347836

More information:

Microsoft TechNet article on this issue: https://social.technet.microsoft.com/Forums/en-US/cf550839-fa7d-40aa-b4ea-c32846cc8659/system-center-2012-r2-endpoint-protection-hanging-on-full-scans?forum=FCSNext

Hotfix: https://support.microsoft.com/en-us/kb/3090303