Thanks much for checking it out! After your response and some additional looking around on our part, we're heading down the "it might be Apple" path - perhaps something that happens on upload from Producer (compression, maybe???).
The reason we're going that way is that we can't really replicate either - without Apple. The upload to the Apple store through Producer seems to be the constant.
So ...
Drop shadows visible directly in .iba file in iBooks Author = yes.
Drop shadows visible in iBooks 2 when using the preview feature in iBooks Author = yes.
Drop shadows visible in iBooks 2 when directly opening the .iBooks file exported in iBooks Author = yes.
Drop shadows visible in iBooks 2 in downloaded preview from iBoookstore = no (only in the TOC view).
Drop shadows visible in iBooks 2 in downloaded (full purchase) book from iBookstore = no (only in the TOC view).
Here's the link to one of the books this is happening to. If you have the time/inclination to look, would you please confirm if you can see drop shadows? There should be at least one on every page of the preview.
http://itunes.apple.com/us/book/u.s.-history-reconstruction/id521396731?mt=13
Again ... much appreciate the look!!!
Jen