Good news, I reseated the graphics card and now it is all working. Very strange. After the first time I reseated the card, it did not work.
Then after the third reseat, it is all working fine. Ran the Apple Hardware test disc, and it came back reporting everything was fine.
I have had it running for the last 3 days and its fine. Even took it through to the Apple warranty centre to check and they could not find any problems.
So guess the card just needed to be reseated.