Regarding the original topic, if you have TweakUI installed make sure that on the General tab that Beep on errors has a check mark. I had the same problem and it was driving me crazy. I found this on the web somewhere and it worked for me.
Mr. K ... is fast user switching on? Try turning it off and see what happens. It sounds like Windows may be trying to send your program events to another user, which is a known oddity in XP.
As far as killing the system beeps ... download Tweak UI if you don't have it already, go into general settings, and uncheck "beep on errors". If you're not registry-shy and don't want to use Tweak UI, I think the key is in HKCU\Control Panel\Sound.
EDIT: Papp, that'll teach me to leave a reply window open while I go to play a game of Natural Selection. Yes, if fast user switching isn't causing the problem, check to see if beep on errors didn't somehow get switched off, since it's a per-user setting.
Also, while I'm here, I'll throw my hat in the ring about the reformatting issue. I've been trying to tell people this for years (including my format-happy girlfriend) ... reformatting is never necessary, save for a few disk-level problems, and if done frequently can potentially cause problems in the long run. If you really want a nice clean install of Windows, pop in a utility boot disk and delete your Windows tree.