When I change a config, add a mod or anything even if it doesn't change world gen I make a new world; So no I don't think it's that. I never make a single test world, every time I launch MC I usually make a new world (I delete the content of my saves folder often).Are you altering the config and then loading an existing world? Cause that would just disable newly generated surface stuff I think, not remove deposits already created. That's my thought anyway.
To give a little more information this is the version of forge I am currently using: forge-1.7.10-10.13.2.1291-universal