Combining transparent pngs - php

Question

I have looked here on SO for solutions for my problem, but I can't find a solution that seems to work for me. Maybe I'm doing something wrong.
I am merging a number of transparent PNGs together, into one display for the customer. There are pretty much three layers (obviously the background is transparent, then fairly rectangular PNGs, but somewhat out of square, and then smaller ones on top of that).
The top layer of smaller images goes on the rectangles nicely. But the rectangles look as though they were filled with black first, then the image applied - you can see this because the image is slightly out of square, so the edges usually have this black line around it. The thing that I don't understand is why this layer has it and not the top - both images are instantiated with the same code.
Here is my code (I found the imagecopymerge_alpha function somewhere, and it seems to do pretty well, but obviously, not entirely).
// Merging:
$this->imagecopymerge_alpha($this->image, $resizedImage, $startX, $startY, 0, 0, imagesx($resizedImage), imagesy($resizedImage), 100);
function imagecopymerge_alpha($dst_im, $src_im, $dst_x, $dst_y, $src_x, $src_y, $src_w, $src_h, $pct){
// creating a cut resource
$cut = imagecreatetruecolor($src_w, $src_h);
// copying relevant section from background to the cut resource
imagecopy($cut, $dst_im, 0, 0, $dst_x, $dst_y, $src_w, $src_h);
// copying relevant section from watermark to the cut resource
imagecopy($cut, $src_im, 0, 0, $src_x, $src_y, $src_w, $src_h);
// insert cut resource to destination image
imagecopymerge($dst_im, $cut, $dst_x, $dst_y, 0, 0, $src_w, $src_h, $pct);
}
// Creating the background/container image:
private function createTransparent($width, $height)
{
$image = imagecreatetruecolor($width, $height);
imagealphablending($image, false);
imagesavealpha($image, true);
$transparentColor = imagecolorallocatealpha($image, 255, 255, 255, 127);
imagefill($image, 0, 0, $transparentColor);
return $image;
}
So, my question is this: do you see anything in here that would make a transparent PNG not maintain it's transparency and merge correctly with a base transparent PNG?