the "Save Layout" option saves the layout of all file Listers and Buttons Banks on the screen, not the icons.
To place the icon onto desktop, press and hold right mouse button over an icon and select "Leave Out". To save the position of the icon, press and hold right mouse button over the icon and select "Snapshot".
You can use "AmiKit:Prefs/Screenmode AmiKit" program to restore the default icons. Simply select the same screen mode as you are using now and reboot your AmiKit. Note: the program overwrites your current desktop icons and uses the default ones instead.
Hope it helps you. Feel free to ask more if necessary.