Well, i turned off, plugged the new drive in, made sure it was jumped to slave. PC booted up and first thing it did was re-configure the disks. It said:

Disk 3: CD-ROM Disk 4: CD-ROM

So it had lost Disk 1: MAIN C Disk, that was fine before i turned PC off and had not picked up the New Disk.
I checked in BIOS, but obviously it could not tell me anything because according to it there were only 2 Disk drives on the system.
So i switched off, unplugged the New Disk and it re-configured back to:

Disk 1: Main Disk Disk 3: CD-ROM Disk 4: CD-ROM

so all was fine again. I have tried it a couple more times, taking the IDE cable out, repluging the hard disks in a different order, checking the jumpers, but no good. I still cant see what the Bios is up to as everytime i plug the new drive in, it loses that and the main drive.