I had the same problem with a nice set of EBC slotted disks and pads. My dealer installed the new discs on the rusty hubs which caused a lot of run out and warped my disks( actually thin spot on rotor). After a while I figured it out and had them turn down the original discs that still had enough thickness. Got a refund for the discs but cost a few hundred to fix the dealers messy install.Oh I have a mile of runout in the rotor. That's why the issue followed the rotor to the other side of the car.
But....you make a great point on the hub. So my initial plan was to check run out on the hub. Right around the studd area. But, I couldn't because of rust build up. The only place I could check it was at the very center. Which didn't tell me much at all obviously.