Thank you all for your observations plus feedback, all very valid possibilities - could have turned out to be any of them.
The actual problem was mentioned in
His Dudeness post below - highlighted - I had not loosened off the Torque arm bolt to Caliper bracket.
Once this was loose the Wheel on its axle was free to slide forward and back in the Swingarm holes and could be correctly aligned.
I think you'll have to re-adjust it. Undo the axle nut and sit on the ground behind the bike and give the tyre a few kicks so the wheel moves forward. Be careful not to kick the bike off the stand. If the wheel moves forward the cover in the swingarm should go back in where it's supposed to be but the chain might go slack and you'll have to re adjust to get the correct slack. Something that's often over looked when adjusting the chain is the torque arm that connects to the rear caliper. It needs to be free to move when you're adjusting the chain. I think it can seize from rust and makes adjusting the chain more difficult.
bandit - your mention of the rear spindle being fitted the wrong way round is also an interesting one.
I've compared it to pics I've taken of my bike in the past, it's been fitted this way in all of them (Nut on right).
Watching a youtube video where someone was removing rear wheel I did notice his nut was on the Left! Had me thinking.