We had the same experience,  they could not find my husband’s mutation.  The kids and I , we have two SW CAH boys, all have a common mutation.  I don’t think they ever found my husbands.  They in fact asked me, in a round about manner, if my husband was the kids father...kind of funny,  if you could see my boys, they look exactly like their Dad. 

They said if they had just looked at my husband’s sample, they would have concluded he was not a carrier.

We had the testing done through Cornell about 7 years ago.