It had assumed a bow in the centre which meant that the rails would not line up with the main running line.
There were a couple of options. Make a new fiddle yard board, trouble here was that I don't have any plywood the same thickness. Secondly, I would have to flatten it somehow. This was the chosen option and so a piece of aluminium ange was cut and screwed to one edge of the piece of board. Happily this would seem to have cured the problem as the fiddle yard now sits square and flat. Not the prettiest of solutions but on that works.