I still want to know more about the site list and where the flow of everything, but we solved our problem. We updated our Agents. We went from the 3.5.5 to 3.6.0. I know we are using older versions, but we are restricted to what is allowed on our network. I am trying to get 4.0 on there (we can't even get 8.5i virusScan yet). If you guys want more details, let me know. Thanks.
Please tell me how you fixed the sitelist issue. I just reloaded my ePO and now it is pushing out the incorrect sitelist. The correct version is on the server, and doing a file search reveals absolutely no files resembling the one going out.
I believe it's contained in the ePO folders somewhere, I've had to re-install ePO 4.0 and 4.5 multiple times and I backed up the folders they state in the KB article, and then restore them after you do the ePO re-install. I've never had that problem before.