requirejs config getting destroyed

gistfile1.txt

// server start up
var requirejs = require('requirejs');
requirejs.config({
  paths: {}, // bunch of paths
  baseUrl: 'dirpath'
});

// request handler
// http request - much more going on here, but this is basically what happens
requirejs.optimize({ baseUrl: 'anotherdirpath', paths: {} }, function () {
  // optimizes sucessfully
  request.reply(); // respond to request
});

// config set in server startup is now gone. all future require's break. :(