Program: 180075
Project: 180075
Buggy source:
public synchronized void convertBlocks(Block thewaterblock){
  int waterid=thewaterblock.getTypeId();
  if ((waterenabled && (waterid == 8 || waterid == 9)) || (lavaenabled && (waterid == 10 || waterid == 11))) {
    Block thegravelblocks[]={thewaterblock.getRelative(BlockFace.DOWN),thewaterblock.getRelative(BlockFace.NORTH),thewaterblock.getRelative(BlockFace.SOUTH),thewaterblock.getRelative(BlockFace.EAST),thewaterblock.getRelative(BlockFace.WEST)};
    if (debug) {
      System.out.println("String_Node_Str");
    }
    for (int i=0; i < thegravelblocks.length; i++) {
      if (thegravelblocks[i].getTypeId() == GRAVEL) {
        if (debug) {
          System.out.println("String_Node_Str");
        }
        if (mcmmomode || getActivationBlock() == thegravelblocks[i].getRelative(BlockFace.DOWN).getTypeId()) {
          if (debug) {
            System.out.println("String_Node_Str");
          }
          if (clayfarm) {
            if (!newgravellist.containsKey(getBlockString(thegravelblocks[i]))) {
              newgravellist.put(getBlockString(thegravelblocks[i]),new ClayDelay(thegravelblocks[i]));
              if (newgravellist.size() <= 1) {
                dispatchThread.interrupt();
              }
            }
          }
 else {
            int rand=generator.nextInt(10000);
            if (graveltoclaychance == 100.0) {
              thegravelblocks[i].setTypeId(CLAY);
              if (customdrops) {
                clayblocks.put(compileBlockString(thegravelblocks[i]),new ClayDelay(thegravelblocks[i]));
                saveClayBlocks();
              }
            }
 else             if (rand >= (10000.0 - (graveltoclaychance * 25.0))) {
              if (waterenabled && lavaenabled) {
                thegravelblocks[i].setTypeId(CLAY);
                if (customdrops) {
                  clayblocks.put(compileBlockString(thegravelblocks[i]),new ClayDelay(thegravelblocks[i]));
                  saveClayBlocks();
                }
              }
 else               if (waterenabled) {
                thegravelblocks[i].setTypeId(CLAY);
                if (customdrops) {
                  clayblocks.put(compileBlockString(thegravelblocks[i]),new ClayDelay(thegravelblocks[i]));
                  saveClayBlocks();
                }
              }
 else               if (lavaenabled) {
                thegravelblocks[i].setTypeId(CLAY);
                if (customdrops) {
                  clayblocks.put(compileBlockString(thegravelblocks[i]),new ClayDelay(thegravelblocks[i]));
                  saveClayBlocks();
                }
              }
            }
          }
        }
      }
    }
  }
}

Fixed version (ground truth):
public synchronized void convertBlocks(Block thewaterblock){
  int waterid=thewaterblock.getTypeId();
  if ((waterenabled && (waterid == 8 || waterid == 9)) || (lavaenabled && (waterid == 10 || waterid == 11))) {
    Block thegravelblocks[]={thewaterblock.getRelative(BlockFace.DOWN),thewaterblock.getRelative(BlockFace.NORTH),thewaterblock.getRelative(BlockFace.SOUTH),thewaterblock.getRelative(BlockFace.EAST),thewaterblock.getRelative(BlockFace.WEST)};
    if (debug) {
      System.out.println("String_Node_Str");
    }
    for (int i=0; i < thegravelblocks.length; i++) {
      if (thegravelblocks[i].getTypeId() == GRAVEL) {
        if (debug) {
          System.out.println("String_Node_Str");
        }
        if (mcmmomode || getActivationBlock() == thegravelblocks[i].getRelative(BlockFace.DOWN).getTypeId()) {
          if (debug) {
            System.out.println("String_Node_Str");
          }
          if (clayfarm) {
            if (!newgravellist.containsKey(getBlockString(thegravelblocks[i]))) {
              if (loadchunks) {
                addBlockToChunk(thegravelblocks[i]);
              }
              newgravellist.put(getBlockString(thegravelblocks[i]),new ClayDelay(thegravelblocks[i]));
              if (newgravellist.size() <= 1) {
                dispatchThread.interrupt();
              }
            }
          }
 else {
            int rand=generator.nextInt(10000);
            if (graveltoclaychance == 100.0) {
              thegravelblocks[i].setTypeId(CLAY);
              if (customdrops) {
                clayblocks.put(compileBlockString(thegravelblocks[i]),new ClayDelay(thegravelblocks[i]));
                saveClayBlocks();
              }
            }
 else             if (rand >= (10000.0 - (graveltoclaychance * 25.0))) {
              if (waterenabled && lavaenabled) {
                thegravelblocks[i].setTypeId(CLAY);
                if (customdrops) {
                  clayblocks.put(compileBlockString(thegravelblocks[i]),new ClayDelay(thegravelblocks[i]));
                  saveClayBlocks();
                }
              }
 else               if (waterenabled) {
                thegravelblocks[i].setTypeId(CLAY);
                if (customdrops) {
                  clayblocks.put(compileBlockString(thegravelblocks[i]),new ClayDelay(thegravelblocks[i]));
                  saveClayBlocks();
                }
              }
 else               if (lavaenabled) {
                thegravelblocks[i].setTypeId(CLAY);
                if (customdrops) {
                  clayblocks.put(compileBlockString(thegravelblocks[i]),new ClayDelay(thegravelblocks[i]));
                  saveClayBlocks();
                }
              }
            }
          }
        }
      }
    }
  }
}