Make sure to download the new Utilities update here (
http://joule.ni.com/nidu/cds/view/p/id/2262). This helps with connection issues to the cRIO-II.
Over the weekend, I experienced problems like this (which are specifically targed by the new Utilities update) when connecting to our cRIO-II. They were cleared up by shutting down all of my network adapters other than the one I was using. Then, I used the Utilities update today as well. After a couple of flashes, it worked properly.