Create library from Existing library - Item vs Document Parent Content Type

Using the option to create from an existing library that has an Enterprise Content Type applied is producing a library with both Document and the desired Enterprise Content Type. To avoid confusion, we delete the "Document" CT leaving just our Enterprise CT. This is now mapped incorrectly to a parent of "Item" vs "Document" or the "Enterprise CT". I suspect it has something to do with the way CTs are pushed onDemand to new sites. If we delete our CT first leaving "Document" CT and then re-add our CT then we have the desired results. Frustrating workaround ...