The issue is a little involved!
My hubs and discs are double drilled to allow for peg drive, which I don't use. When the parts were machined, the machinist couldn't get the disc-to-hub mounting bolts through the holes due, probably, to over-enthusiastic plating of the hub. Rather than re-drill the holes, he used nuts and bolts through the peg-drive holes, which are slightly larger.
The parts were indexed, but when I assembled the hubs I clearanced the bolt holes slightly and assembled correctly using those. I suspect I managed to get some debris between the two, but nothing showed on another dismantling. Another careful cleaning and assembly and it's now fine. I've done a test drive (Silverstone Historic) and all vibration under braking has gone, making it a lot more pleasant to drive.