Every time I exit the subsurface I get all of the resources that I started with duplicated in my inventory. I didn't see any settings to disable it.

Is there anyway to stop that from happening?

Did you try without all other mods?
Could you post a short video of the issue?

Most mods that give you starter kits when first loading the game run everytime the surface is loaded, they do not work well with mods that add new surfaces or planets, my solution? Load your world and then remove the mod that gives you your starter items

Yeah, I think the mod that gives starter items is integral to general game play, but that's a good suggestion...I might try to figure out what mod is actually doing it.