If you follow the guide for creating and deploying certificates you may run into an issue with the SCCM Reporting Point piece of the picture.
https://technet.microsoft.com/en-us/library/gg682023.aspx
When creating the ConfigMgr Web Server Certificate make sure you create a Common Name using the site servers FQDN. If you do not do this, you will be able to see the cert in IIS, but not when you configure SSRS for SSL.