It is a bug that has been around since Presenter 9. Unfortunately there are only two real fixes I am aware of, neither of which are elegant or simple.
1. Revert back to Presenter 8, if you can.
2. Publish the presentation locally and open the viewer.xml file located in the data folder of the published presentation. There will be a line with the notes for each slide. Place where you need a space between the paragraphs. You can then zip the entire output from Presenter and upload it to Connect.
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If you have a space in the PowerPoint Notes in a line between paragraphs, this will preserve the spacing between paragraphs when published.