Most nodes will have two connections between eachother, if you look closely there are arrows at the ends of the connections indicating which direction the connection is heading. Best thing to try is clicking in the middle of the connection to get the one you want. If your still having issues please private message me a pastebin.com of your profile a screenshot of where it is used.
I'm aware of that, and that's exactly what I'm doing. But sometimes when you do that, you don't remove the connection you're clicking on, but another one close to it (not intersecting it or anything). Here is an example of what I mean:
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When I right click on the purple spot, the purple connections get removed before the one I'm clicking on, and the same with the green and orange spots. And when I went to take a look inside the .xml it turns out it tries to remove the connections that are listed before the one you're trying to remove.
So in <Node Id="0" DontConnect=" 1 2 3 4.../> 1, 2 and 3 will be removed before 4 unless they arent close. Also noticed another thing, every time you press Create Arcs it writes every node's neighbors again into the .xml. For example this is what a node from a profile I'm working on atm looks like:
<Node Id="18" Neighbors="17 19 17 19 17 19 17 19 17 19 17 19" .../>
Not sure if this can cause problems, but I thought I'd mention it.
Edit: Did some more testing and the thing about it trying to remove the connections listed before it, isn't exactly true. It sort of seems like problems start to arise when there are connections between nodes of distant numbers. The connection on the picture above is between node 7 and 21, where as I don't have as many (or any at all) problems with nodes which have numbers close together.