Try focusing the top pane on one page and the bottom pane on another page then adding a new comment from the bottom pane... What happens is that you will see the same thing - two comment balloons, one on top pane and one on bottom. If you pay attention when
you start typing the comment you will see that you are typing into the top pane, not the bottom.
This is really annoying because I want to refer to what I was looking at in the top pane while writing the comment in the bottom pane. Instead I have to re-locate the section that was in the top pane.
If I add the comment to the top pane, everything works as expected. I type the comment into the top pane while still viewing the other section of the document in the bottom pane.