Hello,
I want to disable basically all integrations except mekanism so I went to "config/simplyjetpacks-common.toml" and changed the settings to false in there, but on a singleplayer world they still show up with crafting recipes.

I went to the "saves/test world/serverconfig/simplyjetpacks-server.toml" (it was blank) and tried to copy the intergration rules from the "jetpacks-common" file into it, but it clears every time I load the save. I even tried copying the edited server.toml into defaultconfigs and created a new world, but still no.

I have tested this on curseforge in a seperate pack with only this mod and JEI and it still happens.
MC: 1.16.5
Mod Version: 2.6.12.1
Forge Version: 36.2.34

@thatbirdliam A bit late, but for others like me, having the same problem:
Just downgrade to the previous mod version (2.6.11.2) until (if ever) there's a fix. The config seems to still work as intended in that version.