I had the same problem as Jeff, but his solution didn't work for me. I made this script, and it seems to work:
<?php
$img = imagecreatefromgif('in.gif');
$w = imagesx($img);
$h = imagesy($img);
$trans = imagecolortransparent($img);
if($trans >= 0) {
$rgb = imagecolorsforindex($img, $trans);
$oldimg = $img;
$img = imagecreatetruecolor($w,$h);
$color = imagecolorallocate($img,$rgb['red'],$rgb['green'],$rgb['blue']);
imagefilledrectangle($img,0,0,$w,$h,$color);
imagecopy($img,$oldimg,0,0,0,0,$w,$h);
}
imagegif($img,'out.gif');
?>
