Read http://www.mactech.com/articles/develop/issue_16/034-038_Qui..., especially the part that says:

   "Square wave sounds. Unknown to most, the square wave synthesizer never produced
    true square waves. It was more like a modified sine wave. This has been corrected.
    As a result you'll notice that the Simple Beep sounds different. It can now be
    heard as it was originally designed to sound."