[DNSB]

If you use the ePub3 Tools item in the Tools menu and click on Update Manifest Properties, does this correct the error(s) for you. I haven't tried it with a js linked to the nav document, but it works for standard html documents though I seem to recall at one point, reading that what the navigation document can contain is limited and javascript was not listed as a allowed item. Now if I could find that reference...

Edit: The reference basically stated that since the navigation document is intended to be machine readable, javascript should not be used. Instead make the navigation document hidden and create an dedicated for human use html ToC. So perhaps a nav.xhtml navigation document and a toc.xhtml human intended ToC.