No it isn't a bug. A new feature in Kindle 3 is that the header disappears after a short while of opening up a new book so that's just how it works with all the books you read.
I think the idea was to remove distractions from the reading experience and also it does allow the displaying of more text.
Generally I think people tend to prefer this feature over it being always on with previous Kindle versions. Hopefully now you know it isn't a bug, you'll get used to it.
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