Problem with Ligatures / OpenType features...

Hi, I am writing a book using an OpenType font and encountering some problems.
Note - if pics don't show up below, click and they'll "enlarge" and appear.
This type of font has alternates, which can be edited using the "Typography Panel" as shown here:
OpenType fonts, such as Zapfino, have alternate characters. Here's the default settings for this font:
Here's what it looks like when you change the Typography settings...
The changes look fine in iBooks Author, but when I sync them to iBooks on the iPad OR on the Mac, the fonts revert back to their original settings (with different character shapes). I believe this problem just started, and it is messing up my layout a great deal!
When the book transfers to the iPad, it looks fine while the "loading..." screen is there. But as soon as the loading is done, the fonts jump from the chosen "Typography" setting to the default. This happens with downloaded OpenType fonts as well as pre-installed ones from Apple. It also occurs even when I am starting a fresh book from a template, so I don't think my file is corrupt. Any idea what I can do to help?
Thank you,
Stephen

Tom, thank you for taking the time to check whether this works for you. I could have sworn it was working on my projects as recently as a few weeks ago, but perhaps I just didn't notice that when previewing the book on the iPad it was reverting to standard lettering.
I'm not using Zapfino in the book, but I knew it would be a good example since it is a default font. I was under the impression that iBooks supported OpenType features because they allow selection of special typography features  in iBooks Author, those features display in iBooks Author, and there's some mention of turning on/off ligatures at this support site iBooks Author: Change text font, size, color, alignment, and spacing (see 2nd to last paragraph) ... ligatures being in the same panel as the other options.
However, if it doesn't work for you and doesn't work for me... it probably just doesn't work!
Thank you again for looking into this with me

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