Thanks guys for your advice.
I am wondering if that was the case, but now I'm wondering if I have posssibly killed the queen during the cluster capture, version 1.
On the first fine sunny day, (that was yesterday), the hive swarmed and settled in the tree next to the hive luckily.
I caught the swarm and transferred it into a new super, but the swarm was gone the next day. I think it went back under the old hive, so I made a bee vacuum, lifted the hive and caught every bee under the hive.
I Transferred them back into the hive and they seemed to settle down a bit soon after. However late this afternoon I can't even get within 5 metres of the hive and they are on the attack. Guess they may be queenless now.
I will have to check again in a few days when they settle down a bit and carefully search for her. Just when you think everything is ticking along nicely, BOOM.
The good news is that now I have a portable bee vacuum.