Originally Posted by JSWolf
In that case, I think the solution might be very very very simple if the problem is what I think it might be. Go to the Make Sony Reader dialog and then the options tab. Under misc, what are dashes set for? In order to have emdashes, it should be set for "as it is" and then if your text has emdashes, they will come out as emdashes. I'm surprised I didn't think of this earlier.
You were right - that was it. I've uploaded a new version. Thanks for the tip - I wasn't aware of that, not being bothered about the difference between hyphens and dashes personally
. There wasn't a problem with the MobiPocket version - that just got it right first time.