This refers to the new Paperwhite 3G specifically. I don’t know if it also applies to the original Paperwhite, but logic suggests it might well.
If, like me, you’re fond of downloading free, legal, out-of-copyright ebooks, it might come as a surprise, the first time you load them into your Paperwhite 3G, to discover the device won’t display them on the home page.
The problem is that the device doesn’t see the freebies as books. What it does see them as only god and Amazon know (it displays them as “Personal”), but the fix is simple. On the Home page tap My Items. If this is set to Books, set it to All Items.