I think this points to the solution. It seems you must have a title entered on the cover page (dust jacket) in order for the cover itself to be printed.
When I tested a new book layout with a title inserted, as you have done, it worked. It also worked in iPhoto. For my book, my cover was an edge-to-edge borderless image which incorporated an embedded title, so no text actually entered into the text field. I appreciate that this would mean that the title would not appear on the spine, but it seems that a title is also required to generate a printed cover. As soon as I do that, a cover appears in the print preview pdf. So that is the difference. I used the 'modern lines' template and it has worked perfectly this way. So the issue seems to be that you cannot customise your dust jacket and not include a title. This image was previously used as my front cover, text embedded. I will now have to modify the dust jacket layout, using normal text instead.