Here's what I don't understand. I have the so-called cast iron disks on my 900FE but there is never any rust on them. On the other hand, the cast iron Brembos on my 1991 Guzzi Lemans always have a bit of surface rust where the pads don't rub. Are the so-called cast iron Brembos were talking about really cast iron?
Surface rust could be due to the compound of your brake pads. You old pads could have a higher metallic content, so they could be getting embedded into the rotor surface.