It is a known limitation of Windows Explorer - do not use it to view icon files in thumbnail mode. It just displays the last image in an icon file and not the most suitable one.
To view the 48x48 image, switch to "Tiles" view.
Alternatively, you can switch to inverse image order when saving an icon (explore the options at the bottom of the Save dialog). But it is not recommended, because it makes the icon incompatible in normal scenarios.