I don't think I have seen a epub 3.0 file. Can you point me to one to test?
I suspect the cause is the different renderers Kobo use. I believe epubs are read by ADE and kepubs by something else. I don't think the version of ADE they use supports epub 3.0. Kobo announced support for epub 3.0 with the release in Japan. But, I suspect it is only for books they supply. Or only Japanese books.
If you want to test something, change the file extension to ".kepub.epub" when you copy it to the device. The device will treat the book as a kepub and open it with the kepub renderer. I would be interested to know it that picks up the TOC.
Note: I posted about ".kepub.epub" a while ago. A Kobo developer said not to do this this. But, as far as I can tell this is because it can't sync the book to the server. In any case, if there are problems, removing the book should clear it up.