Ok - had another go with this. Booted from a live CD and had a look at the partitioning - may have been trying to boot off a SWAP partition of the second drive - perhaps installer didn't check for boot partition flags? Shouldn't have done as is 2nd drive. Anyway, cleared both disks rewrote MBR and then removed second drive for the moment. Re-installed and we're flying.
Sorry to cause you any work if you'd already started poking around!
Paul