I was copying some files to my friend's Desktop folder, and noticed that one of the files disappeared. I used Terminal's ls command and saw that the file was still there, but not visible in the Finder. After playing around a bit more, I found that files were disappearing and appearing quite consistently.
After trying to set the files' visibility with the SetFile command (included with Developer Tools), I thought maybe the folder was corrupt. So I backed up all the data in his Desktop folder, and then did a rm -rf ~/Desktop to remove the Desktop folder and its contents completely.
I then relaunched the Finder to allow the OS to recreate the Desktop folder. On relaunch, the problem was gone -- and he'd been dealing with this for a year. I couldn't find anything on this in the archives or on Google; hope this helps someone.
[robg adds: Please heed the backup warning -- rm -rf is forever, as they say. I haven't heard of Desktop folder corruption issues, nor did I realize the OS would automatically recreate it if it were missing...]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20050317050850865