I have to second all these posts. I love this program, but it completely looses it's usefulness when I'm trying to edit my friend's arms on her Alex/3px skin. And it is kinda annoying how it doesn't remember the last folder I saved a skin to; I have a very complex folder structure for my Minecraft related files and I usually save skins to the same folder most of the time.
Is the program still being actively worked on, or is it on hiatus? It would be a shame to see such a wonderful project die after it's come so far and been so useful to so many people.
I tried loading my skin, which has the thinner arms, but it only shows with the classic skin type, with the same odd coloured lines that appear when you use the Alex template on an older version of minecraft.