Yeah the problem is you have to treat iBooks as a new completely different reader, insofar as it refuses to follow the ePub specs which everyone else does, case in point, sans-serif fonts inside div, span, p classes...
Once you get it to work and know all the idiosyncrasys of the iBooks, the other readers will fall into place...
eg. this goes from the text to the Notes.xhtml file
<a id="anchor-50-anchor" /><span class="superscript"><a href="Notes.xhtml#anchor-57-anchor">1</a>
This goes from the Notes back to text file
<a id="anchor-57-anchor" /><p class="x-notes-text"><span class="superscript"><a href="Chapter_6.xhtml#anchor-50-anchor">1</a>
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