Some research tells me that Encore, when working properly, will duplicate not just the project, but also copies of the content.
So we're clear, only the content that is in the Encore folders. If the assets used are already transcoded, they will not be duplicated.
But yes, if the assets were transcoded, and are therefore in the Encore project folder, this could be a very large copy.
But on Macs especially, I immediately suspect disk permission issues. I was looking for the Mac equivalent as "run as administrator," and discovered they've changed the Mac troubleshooting document:
http://helpx.adobe.com/x-productkb/global/troubleshoot-system-errors-f reezes-mac.html
I'd try the reset preferences and "Run the application from an administrator account"