If it has dings, even if they are steamed out, the stain will likely soak in different than the non dinged areas due to the crushed grain. It is interesting the dinged areas are lighter though- I would have expected the opposite. Is it possible the damaged areas, being lower than other surface, did not get all the finish sanded off and is rejecting the stain?
I think the best way to deal with this sort of thing, since you are sanding all the finish off anyway, is to spray a sealer coat and then use toner like Mike suggested. That way the surface is irrelevant WRT absorbing stain.