After some testing, I have managed to get the navigation working on my ebook. Before, I had the hyperlinks link to the background images of each page, but I found out that the background image labels cancelled out the hyperlinks on the iPad. This is why the links only worked on one page, as that page didn't have a labelled image anywhere on the page. I then found out that labelled movies did not cancel out the links, so instead of using the background images as links, I created movie widgets, and moved them to the back of the pages as they are not visible, but are still linked. Now the buttons on each page work without any problems.
However, I am still having problems with my table of contents. The way they are generated in iBooks Author makes them hard to customise, and and this point, I don't think that hyperlinks are compatible with the table of contents page. So I will either have to not have a table of contents page, or will have to create a new book to get a table of contents page generated by using sections.
There are also faults with the auto generated contents. Firstly, when all the sections are put into one chapter, the first chapter page does not get linked.
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