So the consensus is that it's the wheels? I know everything flexes, but I just find it hard to believe that the frame flexes. Unless you are a gorilla, it just seems crazy. I can understand a wheel flexing enough though to cause rubbing.
I have a pair of those same wheels and they've been solid for me for 4000 miles. Popped a spoke last week, but threw in one of the spares the wheelset came with and I'm back out riding them. For what I paid for them, I have nothing but good things to say about them. I'm a smaller dude though, so maybe my weight has something to do with it.
I have these wheels and I also ride some Campag Record hubs/Mavic OP rims, some Ultegra hubs/Mavic CXP 33s and some Record hubs/Campag Strada rims on my other bikes. For the price, these Neuvations are pretty nice and I don't notice a huge ride quality drop off on them. I don't know if I am just oblivious or if all of my wheels are pretty nice or if I don't notice it as much because I'm only 145 pounds, but I've never thought, "Wow, these wheels suck, I need new ones."
I've even put my Record/OP wheelset on the bike I ride the Neuvations on and didn't notice much of a difference.