Thanks for the link mariosipad. Unfortunately it hasn't helped me out with my problem. The author says he used a symbolic link to "work around ownCloud’s htaccess restrictions to make the eBook files readable". But I have already tried that and it doesn't work for me.
I will have to look into it further. Owncloud is a massive application, and it's one of those situations where it either "just works" or you end up spending hours or days trawling through manuals.

Looks like I got handed the latter!
Which is typical
Thanks anyway and in the meantime if someone has more advice it will be welcome.