Maybe your line isn't long enough? As in, are you sure it does touch and exceed your figure's lines in two different places (like in #3 point in sixth post in the thread)? :p
Try redrawing the line completely and/or moving it to a different location, then try again. It doesn't happen very often, but occasionally if the positioning of the line and the territory line up in just the right way, it won't work no matter what you do. I can't explain how or why; just give it a shot and see if it works.
If even that doesn't work, you might want to give your SVG to an experienced mapmaker and see if they can fix it for you.
What you need is a hole in the bottom territory for your top territory to fit into. To do that, simply duplicate your top territory, select it and the bottom territory at the same time, and click shift+ctrl+6. Repeat for every territory that needs a hole.