Hm, I don't know GIMP2, but it sounds like you should change some settings ... perhaps the program assumes that you want to save the file in 256 colors only (or the file type can only support this much colors) and changes the color palette!
hmm, usualy when I want to get rid of something I just use "magic wand" with an fuzzy indication (I don't know how it's named in english vesion)
and simply cut and erase the selected area.