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"Well, I am not the original poster, but I can testify it to being true. Friend of mine had the same problem, I had to teach him some basic console commands. It only happened to his desktop files though..."
Are you sure you're not talking about files that are on the hard drive? It is possible to have problems deleting files from the hard drive because of permissions issues.
I am a Mac system administrator and have never come across files not being able to be deleted from the desktop unless they were locked... but thats an easy fix... just get-info on the file and unlock it.
I'm sure it was something simple like that.