Thank you Zoron. Your reply was spot on and helpful, I have now managed to edit the BCD registry and removed the "dead wood" from it. Now the problem has ceased to exist.
Thanks for your reply chunkymonster, but I managed to get rid of it with the method Zoron instructed and I believe I would of have saved a good deal of hassle instead of going the long way.
It does still show I have 'System' on the other partition, but I guess it's only to be expected because it's the primary partition of the hard drive the OS is installed on.
Thanks : -)