icons permanently disappear on desktop

I have a win2k pro workstation that twice now has lost multiple icons on the desktop. I have checked the recycle bin and nothing is there. The first time I was able to restore most of the files using Easy Recovery Pro…however the second time this happened I was unable to find the files using this program. It is obvious that they have been deleted…althought the user swears they did not delete them. I’ve checked for viruses, scanned and removed all or so I think spyware programs. The pcwas shutdown for the night and upon loggin in the user discovered that things were missing…so that would eliminate hacking. Has anyone encountered this before? I’ve checked the whole user profile thing out and it doesn’t seem to be the case. Please help!!!