Okay, before I start posting up the screens, here are the steps I've taken on the client side:
Ran an external scan, checking for issues, using two different services
Checked each and every file for changes that I did not previously make
I had the hosting company (Nexcess), check the physical hardware as well. That was the slowness yesterday. It took several hours to complete, as there is roughly 9.5GB of data (between all the databases) to scan, as well as the physical program files, graphics, and etc.
Nexcess found NOTHING.
Rechecked with Google's Safe Browsing diagnostics today. Results here.
Submitted a dispute with Norton SafeWeb.
Screens of what I did not find. Meaning there are no infections.
Thursday
Friday (yesterday)
One of the subdomains
I have more, but this is enough on the screen end I think.
In the meantime, it appears that IE is having issues with Ajax again.
I would also suggest to anyone getting this error, to disable any toolbars. Those things are prone to infection, and then spoof clean site addresses when trying to infect your machine.