Been playing around with Calibre and plugins, namely Modify epub, Count pages and Quality check. Realised that I had some really bad epubs, although some are quite old (as epubs go). Oh and discovering that epubs are just renamed zip files with the actual text in html format was great. One of my books I'll be reading soon had a non standard character instead of an apostrophe throughout the book. Correcting it was easy.
So given that I've tweaked most of my books, I thought I might as well resend them all to my kobo. So I made the most of it and did a factory reset. Gives me a nice clean database to start from again
We'll see if the problem comes back...
EDIT: just checked the books that were giving me trouble. Cover showed up first time on all the ones I previously had problems with. So whatever was wrong seems to be right again
Thanks again for all the info david.