Set imagealphablending($image,true);
on each new layer.
Try this:
<?php
$image = imagecreatetruecolor(485, 500);
imagealphablending($image, false);
$col=imagecolorallocatealpha($image,255,255,255,127);
imagefilledrectangle($image,0,0,485, 500,$col);
imagealphablending($image,true);
/* add door glass */
$img_doorGlass = imagecreatefrompng("glass/$doorStyle/$doorGlass.png");
imagecopyresampled($image, $img_doorGlass, 106, 15, 0, 0, 185, 450, 185, 450);
imagealphablending($image,true);
/* add door */
$img_doorStyle = imagecreatefrompng("door/$doorStyle/$doorStyle"."_"."$doorColor.png");
imagecopyresampled($image, $img_doorStyle, 106, 15, 0, 0, 185, 450, 185, 450);
imagealphablending($image,true);
$fn = md5(microtime()."door_builder").".png";
imagealphablending($image,false);
imagesavealpha($image,true);
if(imagepng($image, "user_doors/$fn", 1)){
echo "user_doors/$fn";
}
imagedestroy($image);
?>