i've used cj for a while with a lot of different sites, most not registered.
The only times that comm hasn't been counted is by bozo companies -- usually it doesn't matter what the referral url is, as long as a sale is made. However, on occasion, an affiliate link won't be counted by some company that is being a prick about that kind of stuff. So basically, it depends on the company you are promoting (which is a major reason egay isn't on CJ any more)