I have abandoned the factory method for torquing down the head. The 'rotate it through 90 degs' method leaves you with different tourque settings on each both, no matter how careful you are about it.
Can you prove that? I suspect more likely:
a) You have been using heat softened heads and experienced head flutter as the head bolts embed themselves in the top of the soft head at either end of the softened head;
b) You have used a cheap torque wrench or one that has been dropped and is out of specs;
c) you haven't been following the correct technique in tightening the head bolts; and/or
d) you have been reusing the torque to yield head bolts,.
I suggest you have a read of the info here: Tech Tips
and here Tips on Tightening Cylinder Head Bolts
and Bolt Tech Tips
In any event the technique you suggest risks snapping a head bolt.