The problem goes away on earlier versions, so I'm sticking to them.
However I now have another issue with EP, this time in conjunction with the header tag controller. I can see the header fields in admin/products and when I manually enter them they appear. When I download EP, the fields are not to be found. If I enter the fields in the spreadsheet and upload, once again they appear. It's a little concerning that they are lost in the EP download process.
I went down to EP2.41beta7 from 2.60 and it is the same. Any thoughts on this?