The epub checker gave a error on the split_000.html file [element "xxx" from namespace "xxx" not allowed in this context] but that shouldn't have affected the toc since the split_000.html file is the first page and it's a summary of the story with nothing else.
I deleted
http://www.w3.org/1999/xhtml but the toc still didn't appear.
Thanks for the advice guys but for now I'll just use the other app that I can see the toc in.