Whenever I set the nock point a tad too low I get the same thing. Here is my thinking:
When you bare shaft tune, the back of the arrow occupies less space because there is no fletching. When you add fletching you are adding both weight and size to the back end of the arrow.
The added weight will slightly stiffen the arrow, while the added size will often cause too much feather contact.
Because of the above, when I bare shaft I want a tiny bit of nock left and a tiny bit of nock high. Then I add the fletch and check for contact. Usually things are just fine, but sometimes I need to raise the nock point a tiny amount.
I hope this helps a bit..