Personal experience tells me its most probably the setting for the temperature alarm for the CPU. I had the same thing happens to a friends PC. After checking everything and trying all sorts of settings we realised that in the BIOS setup, there was an option that enabled the the alarm to warn if the CPU temperature reached a certain level. We also realised that the temperature set where the alarm would go off was very low so that after normal use for less than 1/2 hr this temp was being reached and the alarm was going off. Its exactly as you described like a siren. Same a like a few of the others mentioned.

Unlikely to be someother error with booting due to problems with mobo or cards or peripherals as these would be beeping - long or short depends on the error. Unlikely t be program also as newer systems wouldnt be using the PC speaker and would most likely be using the sound card output.

wat u need to do would be to check the bios settng for the temp level and set it at something more reasonable or if its already on the high side then u should look into getting extra cooling for the system eg additional fans or something more efficient.

Hope this helps.