Paint3D | program allowing painting textures of different channels | 3D Animation library

The differences in scaling are the result of the fact you're not doing the scaling yourself.

The icon format technically only supports images up to 256x256. You have code to make a square image out of the given input, but you never resize it to 256x256, meaning you end up with an icon file in which the header says the image is 256x256, but which is really a lot larger. This is against the format specs, so you are creating a technically corrupted ico file. The strange differences you're seeing are a result of different downscaling methods the OS is using in different situations to remedy this situation.

So the solution is simple: resize the image to 256x256 before putting it into the icon.

If you want more control over any smaller display sizes for the icon, you can add code to resize it to a number of classic used formats, like 16x16, 32x32, 64x64 and 128x128, and put them all in an icon file together. I have written an answer to another question that details the process of putting multiple images into a single icon:

A: Combine System.Drawing.Bitmap[] -> Icon

There are quite a few other oddities in your code, though:

• I see no reason to save your in-between image as png file. That whole fs1 stream serves no purpose at all. You never use or load the temp file; you just keep using the b variable, which does not need anything written to disk.
• There is no point in first making the icon in a MemoryStream, then loading that as Icon class through its file loading function, and then saving that to a file. You can just write the contents of that stream straight to a file, or, heck, use a FileStream right away.
• As I noted in the comments, Bitmap is a disposable class, so any bitmap objects you create should be put in using statements as well.

The adapted loading code, with the temp png writing removed, and the using statements and resizes added: