I don't believe that the issue is related to upgrade or new installs.
I tested CKEditor on a fresh install of DNN and new install of CKEditor in a clean Windows 7 and Windows Server 2008 R2 environment and across multiple browsers.
I also installed on one existing DNN installation which also resulted in Custom Templates not showing, always shows built-in templates.
The issue that I have already explained is present in every installation that I have tested.
I tested CKEditor on a fresh install of DNN and new install of CKEditor in a clean Windows 7 and Windows Server 2008 R2 environment and across multiple browsers.
I also installed on one existing DNN installation which also resulted in Custom Templates not showing, always shows built-in templates.
The issue that I have already explained is present in every installation that I have tested.