Hi Mike,
Regarding your comment about SC loading jquery libs not being best practice, you are correct that DNN 6 comes with the jquery lib installed but it doesnt come with the "jquery-ui.min.js" lib and the "jquery-ui.css" themes used in the SC popups. We could potentially eliminate loading jquery.min.js but I dont think it causes any issues and loading it ensures that we have the correct version of jquery loaded needed for the SC popups and any references required by jquery-ui.min.js . We tried replicating the issue you reported on 2 different public test portals and the clone popup worked perfectly so their must be something else conflicting in your portal. Did you try clearing the cache in your browser?