Well, if you can see them in the Kindle Previewer or MobiPocket Reader, and they work, then they must be in the .mobi, eh?
Actually I just checked a .mobi book I prepared from an epub via kindlegen, and it had the following guide elements present and functional: Cover; Table of contents; Title Page; Copyright Page; Dedication; Acknowledgements; Preface; and Start Reading.
They all showed up in Kindle Previewer and in MobiPocket Reader. But, on an actual Kindle3 device, all you are ever going to see is: Table of Contents; beginning; (maybe page); cover; end; and location. These are hard-coded into the K3.
So maybe that's why you don't see them when you preview the upload at Amazon, even if they are in the file.
So I'd say, don't sweat it.
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