I have actually had to change how I hold the rest of my fingers on my right hand because playing classical style I have slightly longer fingernails now. And my index finger tip nail had a big tendency to catch all the strings. However before that, when I 1st started out with the new picking method, I too had a big problem with having my index finger middle knuckle hitting the strings constantly and it hurt really badly. I’m going to send you a picture on Instagram of how my hand looks when I hold my pick. Because if I could explain it the best my index finger is really snug tightly curled underneath itself and my thumb is completely over it almost protecting it. My thumb’s fingernail points in the same direction as my index finger big knuckle and practically covers it entirely. I think your situation might be more of a thumb placement than anything else