That's your problem.......

You have the nock point set up according to WHAT instructions?

With the good nock travel of the binary cam bows, even if you are shooting the largest fletching available you shouldn't be hitting the arrow shelf.
Also how are you sure that it's the shelf that you are hitting in the down position?

Set the nock point so that your arrow is dead level and centered with the rest mounting holes. In other words give the bow a level tune.
My guess is that you are simply too far down the string to start with on your nock set.
I start at that point with every binary cam bow I own and have set up and have yet to stray at all on nock set location.

Both points of contact you describe tell me that your sending the arrow away with a launch position that is too low. You should never hit the arrow shelf.