I have no idea what the validator for ebookit.com is based on on, but I know the gist of what you've posted is perfectly valid. Make sure you use the IDPF's validator (
http://validator.idpf.org/) to eliminate any possibility that ebookit.com's validator is the culprit.
I've validated several epub3 documents where the (x)html file and the toc.ncx file were in the same directory. Same basic "index.html#frag" pointing to an element with the id="frag" syntax. It should work fine, so there must be something else wrong.