Epub targets have always been unstable for me, when generated from Flare. For at least five years, Flare has generated ePubs with compressed mime attachment, which violates ePub standards. I have notified them several times and they have not fixed it.

But a more recent problem:

ePubs generated from Flare documents in which equations are used get cut off. Generating ePubs targets with the options to convert "enable MathML to png" selected gives a huge equation image in an ePub. I can make the conversion outside of Flare and set the style option to fix this, but it is broken in Flare. The default with the conversion unselected cuts off the equation, but apparently randomly. The exactly same equation pasted in two different areas will generate problems at one point and none at the other. Here is an example of a file in Flare and the ePub target pulled up in iBooks and Adobe Digital editions for the equation <MadCap:equation>$T_{load}=T_{hold}*e^{\mu\theta}$</MadCap:equation>. I've tried various combinations of with and without the dollar sign and created the formula just using the equation editor, and all have this same issue.