That's interesting, but if i try and change the background color in ANY image editor then it still screws with the color, there isn't any way out! :(
*how* does it 'screw with the color'?
Does the changed image look OK to you visually, or are you saying that the background overwrites parts of the image it shouldn't?
If the latter: Most paint programs allow you to specify a 'tolerance' for a floodfill, specifying how picky they need to be. The smaller the tolerance, the less 'similar' colors it will overwrite in the process during a floodfill.