It appears to me that icons do not stay after snapshot. Unless I missed something.
I've never used OS4, but if this was OS3 or 2 even, then what you're describing is files with no icon image (no associated .info file). Files with no icons cannot be snapshotted as they don't have a real icon in which to save its position. In this case the Workbench uses the default icons depending on the file's type (tool, project, drawer or even disk).