Fixed it. Used dmesg to have a look at 'stuff' with the view to finding out why I could only read the device. Lo and behold there was a line saying that the fat32 was 'broken'. Started to look for Linux solution then thought to use my little netbook (Win XP) and do a chkdsk fix. This fixed the error and when I connected to my Ubuntu machine Calibre found the Kobo.
All is right with the world again :-)
Thanks to all for your suggestions.
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