I have suspected overheating too, even dough the temperatures and fan speed were normal so I removed processor heatsink and fan, cleaned them, put the new thermal compound but no change.
Then I discovered something new, when processor min and max state are at 100% and I disable my internet connection or unplug the LAN cable the beeping stops, I feel so stupid for not figuring this out earlier.
I use the LAN port for internet through Scientific-Atlanta Webstar modem, I tried to change it and even when a use a router to connect 2 computers the beeping continues, so the modem is not causing the sound.
I also tried to restart the computer in safe mode with networking and it still beeps.
I reinstalled the motherboard drivers
even updated BIOS, no changes.
I have also tried experimenting with the processor state and when I set min to 5% and max to 80% I don't notice the beeping, but if I set higher values it beeps.
I am going to try to reinstall Vista and if it's still the same then it's a problem with the motherboard!?
Does anyone have any ideas?