I have the same problem with drop shadows, I don't use them.
Drop shadows not showing up in V.4
I have a few drop shadows in my document. When export a MIB either from ID or the Production tool they do not display on the iPad. It looks like the production tools sees them. I am using the iPad retina templates and exporting to iPad retina. If I turn export PNG off ID freezes. So I am not sure if it's a PNG issue.
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Create transparent box around your object and the drop shadow, then group them. This will allow to show drop shadows.