I'm having the same problem, I noticed this issue mentioning the problem, and attributes it to misusing the new query params API. Where you using the prior implementation?
Edit: My problem was how I was enabling it. I was following the prior method of simply passing a value to Ember.FEATURES:
Ember.FEATURES['query-params-new'] = true;
However, the docs now specify the correct method (which also needs to happen before the Ember js file is loaded by the browser):
ENV = {FEATURES: {'query-params-new': true}};