I had to fix the same issue on one of our in-house CMS, unfortunately I don't know the internals of SS well enough or have time to patch this myself the basic idea below:
Maintain GIF transparency by getting/setting transparent color from source image and copying to destination image
// read gif information to find transparency
$fp = fopen($file_path,"rb");
$result = fread($fp,13);
$gif_version = substr($result,3,3);
$gif_colorFlag = ord(substr($result,10,1)) >> 7;
fclose($fp);
if($gif_version == '89a' && $gif_colorFlag == 1) {
$colorTransparent = imagecolortransparent($src_img);
imagepalettecopy($image,$src_img);
imagefill($image, 0, 0, $colorTransparent);
imagecolortransparent($image, $colorTransparent);
}
If a dev can give this a try and patch SS that be great!