Are you aware that you should NOT uninstall Encore CS6 if you plan to write a DVD or BluRay?
CS6 is the final Encore http://www.adobe.com/products/encore/faq.html
-a workaround for the Cloud http://blogs.adobe.com/davtechtable/
Im not planning to use Encore CS6
It seems to be a bug with the CC desktop app that it isn't properly aware of uninstalled programs. This can be a real problem when you want to reinstall something. Please report it to Adobe.