I haven't gone thru every post in this thread, but I had exactly the same problem in a book I just made.
Each chapter of my book is a different file. I set the start page by taking advice I got here from DiapDealer and Hitch with just the following very abbreviated <guide>:
<reference href="title.xhtml" type="text" title="Beginning" />
<reference href="table.xhtml" type="toc" title="Table of Contents" />
The 60-odd remaining files do not appear in my <guide>.
I made a few .epub-to-.mobi files this way, and of the several I made, only the first I made after that change works properly when it comes to "Go to Beginning."
With the others I get the same problem that prompted this thread, i.e. "Go to Beginning" takes to you the tail end of the file just before the type="text" file.
I spent three weeks getting my book right, and now that one of the files is randomly free of this particular problem, I have drawn the line. I experimented with all sorts of things but without getting enlightened, so am putting it down to a KindleGen bug and leaving it at that.
(Very interested in solutions anyone else finds.)