Could you please upload your savefile (previously, if you have it and after, if you do) and tell me the mods you changed?
I don't have a before save, but I uploaded a save on your github. It's literally any time I alter the mod list, no matter what I altered, once the game is reloaded with the altered modlist, it increments the available belts of each type of resource I already have selected by the number of belts I have of it.