OK, I've nailed down the problem:
If, and only if, the large shape is drawn with the Curves tool
and the points are dragged out to form curved sides, the 3D Body effect fails.
If the large shape is drawn with the Curves tool by simply clicking to create straight sides, the 3D Body effect works as designed:
holes in straight curves.png
If the large shape is drawn with any of the vector shape tools (circle, star, rounded rectangle, etc.) the 3D Body effect also works as designed:
holes in star.png
holes in rounded rect.png
My initial test by drawing curved sides for the large shape was just plain dumb "luck".
Hope this info helps in debugging.
Added:
This applies only to self-contained "holes" in the large shape. If the subpaths extend beyond the edge of the large shape, the 3D Body effect does not work anywhere with more than 3 total subpaths.
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