I did lots of research before posting this, and found quite a few people have experienced the same problem.
So after posting, I decided to phone Apple iBooks support too, and one remark in the conversation we had led me to the solution. It might work for you too:
"...have you double-checked the names of all the files to see if there are characters in there that might mess things up" (not word for word, but you know what i mean).
I did, and there were. I got rid of an asterisk, and a hyphen (both in just one file name) and tried again - and the upload went smoothly straightaway.
It's something you might know, but easily overlook.
Thanks to Sara at Apple for reminding me - and hope it works for you too.