To avoid FR4's Fibre-Expoxy skew, Intel recommand that all PCIe-2/3 differantial paires should be routed in an 10 angle. It's difficult to effectively plow pairs in this angle. We try to use the alternative, routing in normal mode, but rotate whole design before generated out fab data(gerber and drill) using keyin "ra 10". It sounds a good mathod. However, much of opens will occure after the rotation. I have logged this bug in the supportnet. You may try this, and I garantee you should see same symptom in your side.