Ex CJP here. I was a CJP for "x" amount of years before I sold the website.
I spoke to a "high level" CJ employee at CJU a few years ago (anywhere from 1-10 years ago) and they confirmed that upwards of 16% of all affiliate sales are lost (meaning the CJ tracking system fails to credit the publisher accordingly, yet the sale goes through for the advertiser). It's a dirty little secret that they refuse to admit publicly.
There is one MAJOR CJ advertiser, who "x" amount of years ago had such a tracking issue that affiliates did not get proper credit for their sales for a lengthy period of time. The only CJ publishers who actually received an "audit" (in order to determine how much money CJ and the advertiser owed them) were publishers that were CJP's. I know this first hand because I developed a good friendship (both online and offline) with several individuals who worked at this advertiser.
I don't know how CJ is today.....but when I was with them, (going back quite some time), they were in my humble opinion a bunch of "C" rate players, at best.
They purposely hired recent college graduates and paid them extremely low wages, and this was a detriment to publishers such as myself, who continually had to deal with them dropping the ball on certain things.
I had several "account managers" (for both pub and advertiser) tell me that they were over-worked and management gave them too many accounts to deal with.
I'm not knocking CJ, just relating my personal experience.
I also wanted to address the question of cookie stuffing....
A few days ago I needed to find a program for my new computer. I went onto CNET.com and downloaded a "30 day free trial" software with the full intention of buying the software once the trial was up.
Upon installing the software, I saw that CNET (aka Download.com) had a few boxes "checked" prior to the program being installed. They were for "video games" and something else. I unchecked the boxes thinking I was just going to install the program (it was a quasi "major" program, nothing "mom and pop". It was a tool that I needed to use).
After the program was installed, I went into my "uninstall programs" menu on my Windows 7 machine and to my surprise and shock, I saw that either CNET had installed a "coupon" program.....that hijacked both Firefox and IE.
So this got me thinking....was it just this program or was it all CNET programs that installed these "cookie overwrite" programs without your prior knowledge?
I booted up my two laptops, of which I had also downloaded other programs from CNET over the past year, and sure enough, that "coupon" program was installed on my computer.
So I'm willing to venture that at least 25% of all affiliate sales are hijacked in one way or another.