Cecil Adams has something to say on this:
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Bran flakes are fairly dense and they pack themselves close together in the package, preventing the raisins from moving. Kellogg’s simply mixes the flakes and raisins together when filling each box and they stay that way during shipping without much internal migration.
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Which, to me, is kinda not really an explanation. But then he goes on to talk about shelled peanuts in a jar:
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Aristotle, I think, used to wonder about this. Actually there are two reasons. First, while a crumb weighs less than a big piece, the crumbs and chunks in aggregate weigh more per unit of volume. That’s because the big pieces have lots of space between them and the crumbs don’t.
Then we have the mechanics of sifting to think about. It’s easy for the crumbs to slip down past the big pieces to the bottom of the jar, but the big pieces don’t make much headway sinking into the densely packed small stuff. So it’s crumbs at the bottom, nuts on top. Maybe now you have some insight into modern corporate life.
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And you know what? To me that just raises the question about the Raisin Bran again… because the raisins are smaller than the bran.
Now I’m stuck in a circular reference.