Outer layer of skin is transparent with lines around the edges

Put the summary of the bug you're having here

*I created a skin using the new format with windows paint and after trying it as a jpg and png file it has the outer layer of the skin transparent with wierd lines.
Describe what you thought should happen here

After searching around I could not find any info on a fix.
Describe what happened here

Steps to Reproduce:
1. Put a step by step guide on how to trigger the bug here
2. ...I downloaded the reference skin from minecraft.net
3. ...I saved it as both a jpeg and the a png file
4... I opened it with windows paint and set it to be a 64 height and 64 width pixel picture
5.... I followed a guide on how to position the skin properly to make the overlays and such
6... I then uploaded the skin to see what it looked like with the latest snapshot
7.. When it loaded my guy had his inner layer showing with weird lines around him
8. ... I made sure that the skin customization tab said everything was on but it still would not work.