Quote Originally Posted by John Ferraris
Hmmm... I can see your logic, but the beep isn't generated by the sound card, it comes from a tiny speaker plugged into the mother board. I was thinking that *maybe* (but unlikley) the speaker on the motherboard was interfering with some sort of circuitry, possibly on the sound card.

Thanks for the prompt response Z, the plot thickens... ;)
Check your BIOS. There should be two different settings for the CPU/Heat related issue. One will power down your computer if it gets too hot while the other will cause the beep. If you aren't bothering to powerdown your computer when you get the beep anyways, why not just disable the warning function but leave the automatic shutdown function on? If you don't have an automatic shutdown option, check if there is a bios upgrade for your motherboard which does.