Adobe support refused to fix this on the basis that our use case for uploading archives (templates only, no application) is not supported. We use the repository service(superseded) to upload and manage templates that are invoked through the formsservice. As a result one of our developers (we don't have java devs) modified previewArchive.jsp enough to make it work with all the items checked. We then found the ear file to add it to.
I still say if they broke it then they should fix it. If they truly believe there is no use case for it then they should remove it.