That article does not indicate that they had trouble proving damages, it said that they were restricted in the damages they could ask for, and that the difficult issue was proving difficult was proving "subjective bad faith".
That seems to also accurately reflect the most recent action in the case, the order denying both parties motions for summary judgement in January [1][2].
http://arstechnica.com/tech-policy/2012/10/after-five-years-...