Dennis Sweet, meanwhile, explains that similarly strange symptoms can be produced by a different Mac OS X problem:
With Mac OS X, corrupted preference files may not be the only thing to look for.
I have had a weird problem with my Desktop. The problem only shows up with my username, and not any other users on the same Macintosh (a 15' AL Powerbook). The problem would show up when I would download a number of files, usually ten or more, to my desktop. I would then sort them into folders. The problem was evident as:
1. Some files wouldn't show up on the Desktop and/or there would be multiple copies of them.
2. When I transferred the files to folders (usually more than one at a time), the icons would reappear and/or the icons of the files that I didn't copy would move or duplicate on the Desktop.
3. Most of the time, icons that weren't being moved would seem to be duplicated. But if I deleted the duplicate icon, both icons would be deleted.
Selecting Cleanup from the View menu didn't help, even when some of the icons were mostly off-screen.
I just returned from the local Apple Store Genius desk, and the problem was a bad cache file. He deleted the Library:Caches:Desktop folder from my user home folder and I am back to normal. I had spent several weeks trying to find the bad Preferences file to avoid having to do a clean install. Hope this helps someone else.
Also on the same theme, a script for finding bad pref files.