[DerekM]

Notes will be exported as long as they're visible in the document. Not sure off-hand if there's a way to control this if you're viewing notes in a pane. What you need to do before exporting is switch to viewing notes inline (if you aren't already), then Expand All, Select All, Edit Note (cmd-'). Might need to use the Edit Note command twice as it'll probably collapse first if you have any showing already.