Presumably, you want the values in the adjacency matrix to represent weights, some of which could therefore be greater than the number of nodes you have (you might want to scale these weights, I think). If you look at this page, it says that edge weight should be formatted as a "double": http://gephi.org/users/supported-graph- ... sv-format/
Looking at your data file, I see that the edge weights are formatted as integers. You might want to try formatting each edge weight to have a ".0" after it. I don't know if this will work, but it's worth a try. And, perhaps it would help to give your nodes alphanumeric names and give your weights explicit "double" or "float" values.