IBooks author font substitution problem

Hi
Ive now been using IBA for a month or so and have to say its a frustrating piece of software.
This is my latest issue that i cannot resolve.
Ive been building a book for 2 weeks which is at the publishing stage and then all of a sudden when i opened it this morning it tells me that a font is missing and substitues it.
But the font is there and i can change everything back by appending the style sheets. Then if i save and close then reopen it tells me the font is missing again.
I do use Suitcase Fusion but have taken the step to put the fonts i use in IBA only in Font Book as .ttf's.
Also if i open the file on my Macbook, there is no font substitution and the book displays correctly even though the fonts in  Fontbook are the same ones as on my iMac.
(Pulls hair out)!!!!
Anyone have any ideas??

Yes its been working fine in all preview tests on my iPad and others in the company.
Plus my Macbook is a carbon copy of my iMac (i use CCC to clone the iMac HD)
Someone suggested that the two ways to change fonts in IBA causes some differences, apparently the top left dropdown menu when selecting fonts only show whats available for embeding and the drawer you get by clicking the 'A' in the top right shows all the fonts on your system.
Still cant figure it out!!

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