This new thread may be worth a look
http://www.ukgser.com/forums/showthread.php?t=228549
It's not the same problem you seem to have but again shows the disk/wheel carrier (the alloy lump that is splined onto the 'axle' that both the disk and wheel bolt to) can develop a wobble, whether this is always due to play in the splines I'm not sure.
It therefore may be worth checking the disk/wheel runout as this may point to a problem with the carrier. In the event you don't have a dial gauge in your toolkit just bodge a stick (pencil) onto the swing arm with a lump of plasticine or similar so the point just touches the wheel at the edge of the rim. Then rotate the wheel to see if the contact is continous or intermittant, the latter implying a misalignment somewhere. Do the same on the edge of the disk just in case it's the wheel alone
I'm not sure how such a problem would cause the rubbing you describe but it could point to the issue with the carrier being out of true.