I was playing about earlier trying to work it out, it was something that bugged me before but eventually went away. I think it happens when you add new books to collections the only solution seems to be to remove every book in the collection and re add them all at once I think it's best to keep all the books on either the SD card or the main memory and not to split them.
One bad side effect is it doesn't remember which books you have already read.
On the plus side my playing about today led me to discover how to have Calibre add it's own cover images it never did it for me before but now my booklist is looking quite good.
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