stable and es6 code version produce different output

What if you declare b in line 22 var b = require('b').create();, does it make a difference?

No, but a mix version of es6 and stable like this works:

// es6 code version
Modules.addCached("b",(()=>{
  var _b,
      //  b = () => {_b = this;},
      b = function() {_b = this;},   // <---
      pb = b.prototype;
  pb.sqrt = (a) => {return _b._sqrt(a);};
  pb._sqrt = (a) => {return Math.sqrt(a);};
  exports.create = () => { return new b();};
}));
b = require('b').create();
console.log(b.sqrt(3));

I guess it's a special constellation of arrow function usage that causes the interpreter to fail.