The good news is that the new chain has totally eradicated my problem and now fits perfectly.
The bad news is, I now have a problem with the rear derailleur catching on the chain.
It does this until about the 4th cog, the b screw is in as far in as it will go.
Any ideas?
EDIT: I measured the chain by looping around the big ring/large cog and adding a chainlink, the derailleur sits vertical on the big ring/large cog combo.