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The second error is the fault of ePub3-itizer as it creates the nav.xhtml which is needed for the epub3 version (it replaces the functionality of the toc.ncx).
That is a new error message. They are saying It should have an non-empty title but since it is machine readable and titles are not shown, I am not sure why this would matter but they are not treating it like a nav.
Are you running epubcheck on the epub3 version here or the epub2 version here before running ePub3-itizer?
I will probably just add a PlaceHolder text "ePub Nav" to the nav title attribute to prevent this error. In the meanwhile, open the epub3 version of the epub and edit the nav and in the head tag in the title tag place that text.
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