Do you have a second hard drive? If yes, it could be getting spun down when idle, then back up whenever you/Winders tries to access it. If this is what is happening the HDD may be fine, but the soft beep is still suspect.
Check your event log and see if there are errors related to the hard disk. Do you see something similar to below? *Backup your stuff* and run a diagnostic from your HDD mfr. Is the soft beep as loud as the beep when you first turn the PC on? Mobo beeps are usually pretty loud. Is it more of a soft "chirp"? If so it could also be the HDD. Take off the cover and listen to your HDD and fans. Clean your fans if they're dirty (power off, don't let them spin from compressed air if they're plugged in to your PC). Assuming you don't have 3 yr olds to feed it PB&Js, leave the cover off. When the noise next occurs, poke your face in there and see where it's coming from.
Code:
Event Type: Warning
Event Source: Disk
Event Category: None
Event ID: 52
Date: 4/23/2004
Time: 11:22:38 PM
User: N/A
Computer: DELL
Description:
The driver has detected that device \Device\Harddisk0\DR0 has predicted that it will fail. Immediately back up your data and replace your hard disk drive. A failure may be imminent.
For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.
Data:
0000: 0e 00 03 00 01 00 5e 00 ......^.
0008: 00 00 00 00 34 00 04 80 ....4..€
0010: 02 00 00 00 00 00 00 00 ........
0018: 00 00 00 00 00 11 2d 00 ......-.
0020: 00 00 00 00 00 00 00 00 ........
0028: 00 00 00 ...
P.S. Mafai smells