your PaintDotNet.ico is only 16x16, not 256. (but i did find the 256 version in the .exe file, hence i extracted it instead) the best i could find in the source is you Icon50x50.png file under Resources in the source.
my PNG was created with paint.net, so i don't know about the alpha transparency, it works great for me, perfect transparency and 256x256 resolution.