setInterval in module not working

Glad you got this sorted - this is one of the classic JavaScript pitfalls. function() { ... } doesn't remember the value of this.

The easiest way to think of it (I find) is that JS is dumb, and when you use this, JS looks back at how the function was called (and not the function itself):

var a = {
 b :42,
 c : function() { print (this.b); }
};

a.c(); // prints 42
a["c"](); // prints 42
var z = a.c;
z(); // doesn't work

var somethingelse = {
 b :"uh oh",
 c : a.c
};
somethingelse.c(); // prints "uh oh"

However arrow functions do remember the value of this so in your case if you did:

SOUND.prototype.multibeep_works_not = function(freq,time,nr){
  setInterval(() => { this.beep(freq,time); }, 1000);
};

Then it'd work :/