As I was only starting a new shop, which I wanted to configure in the same way as an existing I cloned my existing, and this all works properly. I did find that a couple of modules didnt copy up, this when traced was down to filezilla throwing a 260 error and thinking they were malware, I only updated filezilla a week or so ago, perhaps this has a bearing.? or maybe not! I uploaded the modules via the hosting file upload and worked perfectly, I have parked my 1.6.0.9 install until someone solves the uploading issues.