Oh well, that edit changes a lot.
I have never seen this but that's for sure due to I'm only playing online so I can't rotate the map at all.
However, for two given points, that do not share the same x or y coordinates, there are exactly two possible ways to connect them with a diagonal and a straight.
Either you go the straight way first and then the diagonal way or you go the diagonal way first and then the straight way.
It seems that this is the cause for the diferent looking map graph
However, both express exactly the same as it is only schematic and does not show the actual vehicles path.
I have visualized this by rotating the second image, changing line color from grey to red and overlaying the first image with it. You can see that the same stations are connected, it just looks a little bit different but it's showing the exact same information in a slightly different way.
I would parse that information as "remove that far-away stop in that point of the schedule and add it in between the two stops in the north, where it is much closer to.