If the discs are sitting square and true on the hubs, and the run-out is within couple of thou when measured with a dial gauge, then the only other thing I can think of is that the bracket that holds the disc caliper isn't true to the disc, as Mark says.
I note you've only had one hub replaced - has the other been accurately checked? you only need one side to be out.
My money is on one of the discs not lying absolutely flat and true on the hub, you will get this effect if there's the slightest amount of wobble, even a thousandths of an inch at the hub will produce it.
Either way, it's not going got be anything to do with having narrow wheels.
