Arrgh, frustration.

Hi, all. I've just started using templates for my icons but I've hit a snag. I was working with a base from Angel Sanctuary and the colors all had a rich glow, especially the white shirt of a character. When I applied the template and went to Save for Web, it kept making the shirt and strands of hair transparent along with the bit of template.

How do you get around this?

Thanks for any help!