I had to make sure the software was downloaded and running, the USB disconnected, then connect the USB. Doing things in a different order, such as having the USB connected when running or downloading the software did not work for me.
It also says V 0.6 on the software when my machine was running v 0.6 already. This is a known bug, but I didn't know it was a bug at the time, and found it very confusing. The only way I was sure that the upgrade eventually took was that the "new" v 0.6 had the big number screen as an option.
It also deleted my custom programs, which pissed me off. Don't know if this happened to anyone else. Just note your custom program settings beforehand in case this happens.
You just have to play with it. Its poorly engineered, and it took me 20 minutes, but it will work if you hack at it for a bit. I hope any of this is helpful. I wish I had a cookbook to post, but there is a video I posted in another thread that you can find on youtube that makes the process easier. Googling "Deus II update video" should get you there. Sorry I don't have the link handy.