I found that putting a deranged spray for manes and tails on the whither before riding helps prevent rubbing
You could try a withers free gel pad, so nothing is going to be on his withers
Try an ogilvy baby pad they are cut so that there is tons of extra room for the withers those are the only saddle pads I use on my TB
I had the same problem make sure that your saddle and pads are in the correct position or you could try a saddle pad that is made for high withers
You could try the total saddle fit wither release pads heard those are great!
Make sure you have you saddle pad pulled up off your horses wither or also try find a saddle cloth cut with wither release (I have a leimux one that I really like)