Koyote

Did you miss WhyFi 's post? His point is that seat stays aren't under much stress. In fact, he posted a pic of a Cervelo. Many years ago, Cervelo designed a bike with NO seatstays which was perfectly functional. They didn't mass produce it because the UCI only allows bikes with two triangles.

The point is that, even WITH a mfg defect, a seat stay is unlikely to break. Add in the fact that yours looks like it suffered a trauma, and add in the fact that the company that made the frame (and which is known for honoring warranties, when justified) concluded that it's not a mfg defect, and the conclusion is that it suffered a trauma. You got a replacement because your LBS manager pulled some strings with the company.

I'm reminded of a poster from some years ago, who had bought a new aluminum-framed bike, stored it carefully in a closet while at work, and one day discovered a vertical crease in the top tube -- he posted photos and swore that the dent just materialized out of thin air. He even speculated that a vacuum inside the frame had caused it to spontaneously buckle due to a temperature change. It was all quite hilarious, and easily disproved. And from the photos, the frame pretty clearly fell over (perhaps knocked over by a work colleague) and impacted a countertop or door frame. But this poster was absolutely positive that the impossible had actually happened. (In case it's not obvious: the point of this story is that sometimes **** happens and we're not aware of it.)