epub to .ibooks conversion

Hello!

I have an .epub file, and I want to use this file as a base for publishing with Ibooks. However, while the file looks great in the Ibooks reader, the situation is a disaster when I open it with ibooks author: notice that this is a physics ebooks, so there are lots of formulae, that are seen as images by the epub file (I used a LaTeX to html conversion, and then I imported it to calibre: it works great).

Suggestions are welcome!

Matteo Luca