I tried something this weekend and noticed something interesting. I wonder if anyone else can back this theory up... I previously had the same ad unit (same unit id) on every page of my website and had a decent CPC. At the weekend, I decided to give each page its own individual banner (different ad id per page). The CPC PLUMMETED to an all time low !! Could it be because the impressions will be much less if the unit they bid on only shows on one page instead of a lot of pages ? My guess is that the advertisers have to bid much more if the same unit is on evey page of a website because they are bidding on more impressions and ad real estate per-site ? Just a thought.
I would first ask how your channels are set up? Did you have one channel for that main ad previously? Was it advertiser targeted?