I just got off the phone with GoDaddy Security Tech. He checked the SQL for GoDaddy Hosting, and oddly enough he said there was a Stats Collector in the script/software that was hoarding all the CPU resources.
He obviosuly wasn't allowed to go in Admin and look, but he seemed pretty confident it was a Stats thing that was using up all the CPU.
So the stats thing might be the analytics scripts you've found.