Mac beeping every minute, exactly
SoundBunny is a new app that I have just learned about. There is a free demo available which will work for 15 days (I think).

The app window will show you every app which is makes a sound. That might help you track it down.

You can also tell it to ignore apps which you have ruled out, which should help you narrow things down a but too.

I hope that helps.

(n.b. I am not related to this app except as a customer. The purpose of SoundBunny is to let you set the volume for each app, but I thought it might help with this as well.)