You are absolutely correct. The only thing that really matters is real
life processing power, like you said. The problem is, right now, for
the same price you get better real life performance from Intel. All
the technical talk (native quad myth) doesn't help much if your
product doesn't deliver the performance.

As for your own story, are you sure your application is fully multi-
threaded (it should be as most scientific applications are). If,
however, it's not, then it's only logical that AMD would outperform
Intel.