I finally found an old thread that discusses this cursed beep that has been haunting me
My car is seeing the mechanic this week and I will tell him to examine the brake and clutch booster hoses to make sure that they have a check valve.
Is the car really knocking when it beeps, or does the beep have nothing to do with actual knock occurring? My car just started to do this after I had the 'free boost mod' done to it.