I have never used minecraft skins editor, so I'm not sure how exactly to fix this using that program. But it appears the transparency of the entire skin is colored in as white.
Generally I try to leave everything that isn't part of the skin transparent.
When I run into this issue I get out GIMP or photoshop. You can use the select tool or eraser to decolor the background and transparent parts of the hat areas.
If using GIMP (it's a free download) you will need to "export" and make sure "save color values from transparent pixels" is clicked.
Sorry I couldn't help you with what's causing the issue in the skins editor you do use, but I hope I have at least helped you fix it using other methods.