problem fixing pinchushion on Samsung TX-R3079 CRT HDTV

This TV had a noisy part near the flyback (as far as I can tell, thought it's hard to be sure, is that it's a small transformer right next to the flyback, but I don't think it's the h-drive transformer) that seemed thermally sensitive- it would start squealling after running a few minutes, and stopped once when I freeze-sprayed it). All this time the picture was fine. So I replaced the deflection board w/ a refurbished one from parts.com. New board has OK focus and colors but geometry was off (I expected it would have to be adjusted). So went into the service menu using the remote control, to setup size and distortion. All the items excetp horiz-amp (gain) and horiz-parabola (pincushion) worked OK, but those 2 had no effect on the screen. why would that be? does it make sense to put the old deflection board back in, very OK geometry, and then swap out the noisy transformer from the new board? other ideas welcome! I understand electronics, but have no TV experience or test equipment. Thanks in advance for anything!