Coincidence? THey are seperate programs.
Was your CS6 version a perpetual one? Maybe the CC updater wants to apply a PS CS6 CC only update on a version that is not a CC one.
Hope that you did follow me. Uninstall CS6, and reinstall the Creative Cloud version of CS6: http://blogs.adobe.com/vikrant/2013/09/can-i-install-both-cs6-and-cc-apps-on-my-computer/