>Sometimes when I click on the Global Refresh button, the new messages appear in the bottom pane instead of the top pane. I finally stumbled onto what I have done differently to cause this.
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>When I click on the refresh button, it works as expected and the messages are in the top pane. When there is a number other than 0 to the right of the button, it becomes a hyperlink and when I click on that the messages show in the bottom pane.
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>Does this happen to anybody else?

Yes, this is the correct behavior. That option, the link on the number, is there to allow the viewing of new messages in the botton frame without affecting the current messages as well as without reseting the counter of new messages.

The regular refresh button will provide the default behavior thus reseting the counter of new messages and displaying them in the upper frame.