It wasn't really shown to be faster; see http://www.scottaaronson.com/blog/?p=1400. To focus on the "3600 times" issue, I suggest searching for the strings " Ising" and "CPLEX". Don't miss the extremely thorough discussion in the comments, which includes comments from Cathy McGeoch (the author of the "3600 times" work), Peter Shor (as in Shor's factoring algorithm), Scott Aaronson, Greg Kuperberg, and many others.