I wonder if it's because they used to consider the sweat test to be the gold standard when it came to CF testing. They did the same thing to us when DS was diagnosed. He'd actually had two genetic tests -- local hospital and then at the Children's Hospital where he had surgery to correct his bowel obstruction surgery. We'd gotten the test results back showing positive for CF and a few weeks later they did a sweat test, which came back normal.
They also did a poop test to see how much fat was in his stool. At that point, our CF doctor had taken over his care and pretty much shook his head. Said something to the affect that "we already KNOW he has CF and we already KNOW he has enzymes because malabsorbs". I think the CF dietician was behind the testing for some odd reason. Maybe because it was just their standard protocol. Who knows.
I'd started accepting the CF diagnosis and then when the Sweat test results came back, I kept thinking in the back of my mind that maybe he DIDN'T have it. Took me several months to believe he had it. We still continued with his meds, cpt, preventative care, hoping that maybe it was all wrong...