I can't comment on the USB problem you're having because I use the optical out from my macbook pro. I think it sounds just a wee bit better. As for the app nap, I'll have to do a bit more looking around. I still have the app nap option for all the other apps that had it before, so I suspect this is to do with A+. Like you, I do not have an app nap option for Audirvana Plus. It might be worthwhile uninstalling and then reinstalling A+ if you're having trouble with it. It is performing fine for me.
Edited by snowshoe - 3/3/14 at 7:50pm