hda_beep beeps with wrong frequencys, e.g. when it should beep with 100KHz, a very low pitched tone sounds, and when it should output 100Hz a very high pitched tone is audible. The scale isn't just reverse, it seems to be non-linear, e.g. a sound that should be 2KHz (but isn't) and a sound that should be 3KHz (isn't either) do not sound like a difference of 1KHz. This was tested with "beep" http://johnath.com/beep/beep.c which works correct with a real hardware system-speaker.
Fixed in sound git tree now. commit fa7979663190240b838ab8c8bad7f59e618bf77c Author: Takashi Iwai <tiwai@suse.de> Date: Tue May 19 12:50:04 2009 +0200 Thanks for reporting.