Most likely it's because of the difference of mass between the Shuttle and the Ares. More mass makes pogo less of a problem.
These types of problems are going to pop up with any new program, and the media is going to blow it out of proportion.
I agree, it certainly sounds like NASA is taking all the right steps. You make a preliminary design, analyze it and improve it. If this is something that should have been anticipated before the original drawings were begun, that's a bad thing but not a disaster.
All in all, it's merely an uncomfortable stumble, but not really anything like a major embarassment.