Try asking on the ame forum:
http://forums.adobe.com/community/ame
In a related thread there, it points to this:
http://helpx.adobe.com/premiere-pro/kb/features-presets-missing-premie re-pro.html
It probably doesn't matter, since the solutions are probably the same, but I'm suggesting you not focus on Encore because Encore is not "the application that installed" AME. I think of that as Premiere Pro or the entire suite. I think the error comes from an issue in PR's activation. I realize it shows as activated for you.