It could be in the torch body. Is the taper relative to the same side of the table? If something is not set right with the swirl ring, that could push the taper in one direction. Try the cut again with the same parameters but turn the part 45 degrees, this way both x and y motors are counting/turning. If the problem moves or is cut in half it could be motion. If it covers the same area as the original (half of one side and half of the other) then it could be torch. Are you the original owner of the 1250? I had looked at used machines and found that water damage in the torch cable was common.
I have cut some 12ga over the last few days and found that the taper was considerably more than on 1/2" or 3/4". Over half inch you can consistently get under 2 degree taper. I was surprised to find how hard it was to get good cuts on thin stuff. All that said, the taper was even all the way around the parts.
I offer that as food for thought. I am relatively new to CNC. So I could just be rambling.