FYI, I'm having the same problem. I have finally managed to create an EPUB file that makes it past validator.idpf.org/. I used KindleGen to create the mobi but every time, it opens almost at the end of the book.
The following is the fourth line in the <guide> in the content.opf:
<reference type="start" href="foreword.xhtml" title="Beginning" />
However, of the almost 60 .xhtml files that make up my EPUB content, it is the second-to-last file:
<reference type="text" href="xxxx.xhtml" />
that becomes the default start page: where the book opens when you open it on the Kindle, and where it goes when you select "Go to beginning."
I don't know if this info is going to help solve the problem. I haven't delved into the matter of anchors brought up earlier in the thread, but surely - in theory at least - my .opf's type="start" should be sufficient.
(Have been at this for 15 hours straight today - totally bug-eyed now - off to bed...