This script worked fine in 4.0.4, but produces a bad color-shift in 4.0.6:

$srcImage = ImageCreateFromJPEG( $srcImgName );
$dstImage = ImageCreate( $dstWidth, $dstHeight );
ImageCopyResized($dstImage, $srcImage, 0, 0, 0, 0,
   $dstWidth, $dstHeight, $srcWidth, $srcHeight);
ImageJPEG( $dstImage, $dstImgName );

Using the new 4.0.6 function ImageCreateTrueColor() instead of ImageCreate() on line 2 fixes the problem. 

I wanted to let you know about it in case the underlying changes in GD that caused this problem might cause other similar problems. 

It might be useful to return ImageCreate to its previous functionality and add an ImageCreatePalette to go with ImageCreateTrueColor. Just a thought. 

Thanks.