With recent versions of Apple Mail, the Page Down key always applies to the message content pane (unless no message is selected), even if the message list had focus. However, you used to be able to type Control–Page Down to make it apply to the message list. This no longer works in OS X 10.9. Is there another way?
I wrote some AppleScripts that can Page Up/Down in Mail’s message list, and the scripts can be assigned Control–Page Up/Down as keyboard shortcuts.