Remember KB931125? The patch that broke tons of Configuration Manager management points? Yeah, that one. I just found out that as of October 17th Microsoft has released a “quick fix” for this problem so that you don´t have to manually delete the certificates yourself. Basically the fix will delete all the third party root certificate authority certificates installed on your computer/server and then download the ones needed.
Check out KB2801679 for more details. You can also read about the root cause of the schannel error in the article.