I was really confused when Nitro went over Punk. I suppose they're just building to Punk's eventual (hopefully) win, but you're right. CM Punk made Nitro his bitch just a few months earlier, and now he's suddenly so much more bad-ass?
On the plus side, I hated Johnny Nitro's entrance music so much, that it gave them a reason to finally change it. So I guess it worked out alright, in that respect.