If nothing bad is actually happening, I wouldn't worry about it too much. Since it only happens once in a while, if you want to really fix it it'll take some research.
First, get yourself a copy of asus probe (probably on your mobo CD, if not, on Asus's website.) Install that, then run it and turn on "History" and set it to log everything it can. Then, wait till it beeps (random beep I mean) and check the history to see if it recorded some sudden drop in fan speed or spike in processor temperature or anything like that.
If it doesn't find anything, or if you just don't want to bother with it, you could always just unplug the PC-speaker
