Guys,
Figured this out finally.
After talking to a so called techie at the place where I got the controller card from he suggested that I talked to Samsung and get the drivers for the HDD.
He was talking right out of his backside because it was causing issues whether the HDD was plugged into the card or not.
So today I copied over the driver files from the driver CD for the card, took the card out of the system, booted up using the Windows CD, pressed F6 on the setup screen installed the drivers for the card, switched the system off, inserted the card, rebooted and hey presto the card is alive, so after much sweating and sighing I managed to resolve my own problem.
Many Thanks to the above people for the various suggestions.
Cheers