Apparently this is a color profile issue. Something to do with the image being of one color profile, whereas gd only lets you save your image in the one color profile it knows how to save images by which differs from the inputted image's, resulting in the colors looking different.
It seems you are going to need to use imagemagick to not have the colors changed. You should read these:
http://www.zenphoto.org/support/topic.php?id=3582
http://devot-ee.com/add-ons/support/ce-image/viewthread/1085