This will probably be best answered in the Mobi or Calibre forum, but the short answer is; the TOC is probably at the end of the book because that's the default behavior when you convert an epub to mobi with calibre.
You're really talking about two different things. The "Go to>Table of contents" just jumps to the html version of the TOC... wherever it is in the book. So if you want it in the front, add an html TOC to your original source (before the preface) and tell calibre (if that's what you're using to convert to mobi) to NOT automatically add the table of contents.
With mobi, the toc.ncx file is only used to create/facilitate the chapter "jump points" on the progress bar. They allow you to jump to the various chapters with the joystick/d-pad.
Last edited by DiapDealer; 07-15-2011 at 01:44 PM.