It's not clear to me from your answers whether you tried setting Keep with Next to 0. The way your Keep Options screencap shows it, you have each BODY paragraph keeping with at least 2 lines of the following paragraph. This would force one line to the top of the page, since there's not enough room at the bottom of the previous page for the last line plus two more.
In general, you should set Keep with Next to 2 for heads (not body copy), so that heads don't end up lonely at the bottom of the page. In general, you should set body copy to Keep lines together, usually 2 at start and end, but set Keep with Next to 0, so ID can break between graphs.
Something else I've noticed about footnotes: once in a while ID gets "stuck" in a certain pagination, even though you might make changes that should cause it to reflow. To force it to reflow after making changes, cut and paste the text that you want to reflow.
Ken Benson