I recently ran into an issue where a web service that I had set up through SharePoint was throwing the error: “The root of the certificate chain is not a trusted root authority” The web service ultimately sent out an email with an attachment that is retrieved from a SharePoint document library. The error was occurring when I created a HttpWebRequest and called the GetResponse method. Initially, I tried to reassign the ServicePointManager.ServerCertificateValidationCallback property to a method that just returns true, but that didn’t seem to work.
Eventually, I found this blog post: http://godwinsblog.cdtech.in/2010/12/sharepoint-2010-root-of-certificate.html that had me download all the certificates in the SSL certificate chain and add them into SharePoint. After adding the root, intermediate and SSL certificate the web service started working properly.