Thanks for the reply davifor. You were correct, there was an alphabetically first in the list pdf that the Kobo choked on (though it displays correctly in evince, the gimp and all other softwares I have on this box that open pdfs (go figure)).
Interestingly, the cover jpg shows as a separate publication when doing a manual copy rather than a Calibre transfer -- jpg is not on the list of supported formats for this device.
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