Ok, I sorted it out eventually.
The WD disk I made didn't work when I got it home
I booted to the Windows setup CD and ran the recovery console. The repair tools are still available even thought there is no windows installation.
Chkdsk showed unrepairable errors on C:\ but a chkdsk/r sorted that.
Anyway, I discovered that for some reason, setup wanted to write the setup files to one of the array disks which I hadn't noticed before.
So I disconnected the array disks and setup ran perfectly.
I have no idea whether the Raptor needed that chkdsk/r or not.
Anyway, job done
