Sorry to reply only now, I missed the fact that you edited your initial post.
Anyways, the reason for your problem is the fact that your GraphML is invalid: all edges have the same id. To fix the problem, ensure that edge ids are unique. The easiest way to do so would be to open the file in an old version of yEd (e.g 3.1) and simply save the file using a different file name. Alternatively, you could open the file in a text editor or XML editor and change the ids by hand.