Would need to the see opf in order to give any real advice... but:
The page map thing you can safely ignore. As for the guide items, I'm not sure what the 'notes' item is, but I doubt that mobi supports it. The 'text'-type reference item can be used to tell the reader where to open the very first time, but without seeing the opf file, it's pretty hard to see what may be going wrong.
Last edited by DiapDealer; 03-05-2012 at 05:56 PM.