In my opinion, I think that while CJ is down and stats are still 'tracking', it's not 100% tracking. I say this because it seems like everytime stats/sales are down, we come in with a below average day. Everytime!
To boot, this 'upgrade' is terrible. I worked at a high tech company for four years, and we tested everything in QA before it went into production.
Your QA, testing system, is an exact mirror of your production system. You test in QA and get all the bugs out, then move all your changes into Production. Everything should work great, because your QA database is an exact copy of your production database.
This is techinical changes 101. CJ must test in the dark, because these changes do not work, which leads to reduced sales, unhappy affiliates and publishers. I am calling my rep tomorrow, for sure.