Could it be that the patches are a slightly bit different in thickness?
Most certainly that will change POI. Or one compresses easier than the other. Or dif weaves.
Or one more absorbent.
On the thickness, only way to tell is mic it yourself. Mic it loose then tight. I have never in
over 40 yrs bought patch that was the thickness it was stated to be.
I think if they are Exactly the same material, square or round will not make a dif.
Unless, your barrel just don't like squares
Now a dif size could possibly make a dif, because the excess patch may be sealing around
the edges of the ball better/more. A Crono could tell you that as the better seal will have more
velocity.