OK, that one worked.
Not sure what was wrong the first time, but it was giving me an invalid version error.
Inspecting the save game I understand what's happened, and there is one slightly dubious quirk. When producing a settler food is converted to additional production, so you have an effective production of 10 per turn when building settlers. 4 hammers go to completing the current settler, and the remaining six overflow to the next turn. The only slight oddity is that you still get the full six overflow production even if the next project is not a settler, even though they started off as food
I'm not entirely sure if this is intentional, but this is the fairest way of doing it I think. The overflow food/production should not be lost on completion of the settler, so it seems fair the next project should benefit. I suppose you could have a system where overflow food goes in the food box and overflow production to the next project, but this is the kind of change that seems likely to be unnoticeable and potentially problem causing.
Again I don't think there's anything that needs 'fixing' here.