I think it unlikely the new transformer is incompatible but what might have happened is the old one damaged some other part of the circuitry, particularly if it 'flashed over' (sparked because insulation failed). Tell me the model number and I'll see if I can find a schematic to help narrow the problem down.
I'll try to explain what I think has gone wrong: The electrons that light up the screen start their life in the beck of the CRT, right at the back of the TV. The high voltage on the CRT makes them rush toward the front of the screen where they hit phosphor paint dots which glow and produce the picture. The electron beam is made to sway side to side and up/down (aka scanning) so they trace a path across the front glass by making them pass through a magnetic field. The field is created by the two coils of wire surrounding the glass neck of the CRT, one bends the beam so it reaches the top and bottom of the screen, the other bends it so it reaches the left and right sides. Working together they make the beam go side to side rapidly and top to bottom more slowly so the 'raster', the area of the picture itself is scanned by what looks like 525 or 625 lines, depending on the TV standard used in your country. While that sounds fairly easy, there is a catch, the distance from where the electrons start to the corners of the screen is longer than the distance to it's middle edges. So the lines at the top and bottom need more scanning power than the ones across the middle of the picture. To achieve this, a small amount of the vertical scan signal is used to adjust the width scan signal, it basically tells it the picture SHOULD be bowed in at the sides to compensate for the extra distance to the corners, the shape of the glass corrects it back to square. I think the problem on your TV is the circuitry that dynamically adjusts the width to do that isn't working properly.
Brian.