Zahid,belonging to this part of the world maybe I can understand your problem better.
I presume that you have specs (from your consultant) where the pipe is already designed for pressure. so that's not a concern.Now if you are using B31.3 it does not check stresses for allowable case (prior to 2004 edition).So how are you comparing operating case stresses?Are you using the 2004 edition.
Most probably there is some problem woth supports or wrong densities.Again wrong densities will make your system fail all along it's length (almost all nodes if not all).If your system if failing at certain nodes then please provide supports near that point.
I feel you are from an operating plant.Are you really required to do stress analysis yourself.Otherwise why don't you throw this to your detailed engineering contractor.I always wanted to be on client's side for that reason.
Another thing don't get discouraged form some hard hitting replies.These are the people we have to learn from.
Thanks Mr Breen for not only sending good replies but also the encouragement to young engineers.I remember three years back I was in tough situation and I could convince my client only after showing your reply to them.
Regards