Program: 80792
Project: 80792
Buggy source:
public static void preInit(){
  if (PAConfig.allowWoodenLevel)   woodUpgrade=new ItemWoodUpgrade();
  if (PAConfig.allowStoneLevel)   stoneUpgrade=new ItemStoneUpgrade();
  if (PAConfig.allowIronLevel)   ironUpgrade=new ItemIronUpgrade();
  if (PAConfig.allowDiamondLevel)   diamondUpgrade=new ItemDiamondUpgrade();
  if ((PAConfig.allowCobbleUpgrade) && (PAConfig.minerEnabled))   cobbleUpgrade=new ItemCobbleGenUpgrade();
  if ((PAConfig.allowFillerUpgrade) && (PAConfig.minerEnabled))   fillerUpgrade=new ItemFillerUpgrade();
  if (PAConfig.allowWitherUpgrade)   witherUpgrade=new ItemWitherUpgrade();
  if (PAConfig.allowCoalPellets)   coalPellet=new ItemCoalPellet();
  if (PAConfig.rfSupport) {
    rfEngine=new ItemRFEngine();
    CheatRFEngine=new ItemCreativeRFEngine();
  }
  Item previousTier=Items.redstone;
  if (woodUpgrade != null) {
    woodUpgrade.preInit(previousTier);
    previousTier=woodUpgrade;
  }
  if (stoneUpgrade != null) {
    stoneUpgrade.preInit(previousTier);
    previousTier=stoneUpgrade;
  }
  if (ironUpgrade != null) {
    ironUpgrade.preInit(previousTier);
    previousTier=ironUpgrade;
  }
  if (diamondUpgrade != null) {
    diamondUpgrade.preInit(previousTier);
  }
  if (witherUpgrade != null)   witherUpgrade.preInit();
  if (fillerUpgrade != null)   fillerUpgrade.preInit();
  if (PAConfig.rfSupport) {
    rfEngine.preInit();
    CheatRFEngine.preInit();
  }
  if (coalPellet != null)   coalPellet.preInit();
  if (PAConfig.enableWitherTools) {
    witherWood=new ItemWitherWood();
    witherStone=new ItemWitherStone();
    witherIron=new ItemWitherIron();
    witherDiamond=new ItemWitherDiamond();
    witherWood.preInit();
    witherStone.preInit();
    witherIron.preInit();
    witherDiamond.preInit();
  }
}

Fixed version (ground truth):
public static void preInit(){
  if (PAConfig.allowWoodenLevel)   woodUpgrade=new ItemWoodUpgrade();
  if (PAConfig.allowStoneLevel)   stoneUpgrade=new ItemStoneUpgrade();
  if (PAConfig.allowIronLevel)   ironUpgrade=new ItemIronUpgrade();
  if (PAConfig.allowDiamondLevel)   diamondUpgrade=new ItemDiamondUpgrade();
  if ((PAConfig.allowCobbleUpgrade) && (PAConfig.minerEnabled))   cobbleUpgrade=new ItemCobbleGenUpgrade();
  if ((PAConfig.allowFillerUpgrade) && (PAConfig.minerEnabled))   fillerUpgrade=new ItemFillerUpgrade();
  if (PAConfig.allowWitherUpgrade)   witherUpgrade=new ItemWitherUpgrade();
  if (PAConfig.allowCoalPellets)   coalPellet=new ItemCoalPellet();
  if (PAConfig.rfSupport) {
    rfEngine=new ItemRFEngine();
    CheatRFEngine=new ItemCreativeRFEngine();
  }
  Item previousTier=Items.redstone;
  if (woodUpgrade != null) {
    woodUpgrade.preInit(previousTier);
    previousTier=woodUpgrade;
  }
  if (stoneUpgrade != null) {
    stoneUpgrade.preInit(previousTier);
    previousTier=stoneUpgrade;
  }
  if (ironUpgrade != null) {
    ironUpgrade.preInit(previousTier);
    previousTier=ironUpgrade;
  }
  if (diamondUpgrade != null) {
    diamondUpgrade.preInit(previousTier);
  }
  if (witherUpgrade != null)   witherUpgrade.preInit();
  if (fillerUpgrade != null)   fillerUpgrade.preInit();
  if (PAConfig.rfSupport) {
    rfEngine.preInit();
    CheatRFEngine.preInit();
  }
  if (coalPellet != null)   coalPellet.preInit();
  if (PAConfig.enableWitherTools) {
    WitherTools.preInit();
  }
}