This is the expected behavior. Apple Network Assistant is designed to leave any items on the desktop alone, both on the client and on the administration computer. There are a couple of situations where this functionality comes in useful:
- On the client, when there are things you want to keep safe and do not want replaced or erased when you copy the entire hard disk.
- On the server, when there are just a few of things you do not want to copy to the client systems (administration applications, for example).
If your lab computers have items on the desktop and you want all of them to start off with a clean hard disk, use Network Assistant's Delete Hard Disk feature before copying the hard disk. This erases all items on the hard disk (except for the System Folder), including anything on the desktop.