Program: 98004
Project: 98004
Buggy source:
public static void main(String[] args){
  int MAX_LEN=20;
  Random R=new Random(0);
  String dbName="String_Node_Str";
  ZooConfig.setFileManager(ZooConfig.FILE_MGR_IN_MEMORY);
  ZooHelper.createDb(dbName);
  PersistenceManagerFactory pmf=JDOHelper.getPersistenceManagerFactory(dbName);
  pmf.setConnectionURL(dbName);
  PersistenceManager pm=pmf.getPersistenceManager();
  pm.currentTransaction().begin();
  TestClass t=new TestClass();
  pm.makePersistent(t);
  pm.currentTransaction().commit();
  pm.currentTransaction().begin();
  Query q=pm.newQuery(TestClass.class);
  for (int i=0; i < 100000; i++) {
    StringBuilder qs=new StringBuilder(1000);
    int len=R.nextInt(MAX_LEN);
    for (int j=0; j < len; j++) {
      int p=R.nextInt(FILTER.length);
      String s=FILTER[p];
      qs.append(s);
    }
    String qss=qs.toString();
    int nArg=0;
    int posArg=0;
    Map<String,Object> argMap=new HashMap<>();
    while ((posArg=qss.indexOf("String_Node_Str",posArg)) >= 0) {
      posArg++;
      argMap.put("String_Node_Str" + nArg,nArg);
      nArg++;
    }
    try {
      q.setFilter(qss);
      if (argMap.isEmpty()) {
        q.execute();
      }
 else {
        q.executeWithMap(argMap);
      }
    }
 catch (    JDOUserException e) {
    }
catch (    NumberFormatException e) {
    }
catch (    Throwable e) {
      System.err.println("String_Node_Str" + qss);
      for (      String key : argMap.keySet()) {
        System.err.println("String_Node_Str" + key + "String_Node_Str"+ argMap.get(key));
      }
      throw new RuntimeException(e);
    }
  }
}

Fixed version (ground truth):
public static void main(String[] args){
  int MAX_LEN=20;
  int N_TEST=1000000;
  Random R=new Random(0);
  String dbName="String_Node_Str";
  ZooConfig.setFileManager(ZooConfig.FILE_MGR_IN_MEMORY);
  ZooHelper.createDb(dbName);
  PersistenceManagerFactory pmf=JDOHelper.getPersistenceManagerFactory(dbName);
  pmf.setConnectionURL(dbName);
  PersistenceManager pm=pmf.getPersistenceManager();
  pm.currentTransaction().begin();
  TestClass t=new TestClass();
  pm.makePersistent(t);
  pm.currentTransaction().commit();
  pm.currentTransaction().begin();
  DBLogger.setLoggerLevel(Level.OFF);
  Query q=pm.newQuery(TestClass.class);
  long t0=System.currentTimeMillis();
  for (int i=0; i < 100000; i++) {
    StringBuilder qs=new StringBuilder(1000);
    int len=R.nextInt(MAX_LEN);
    for (int j=0; j < len; j++) {
      int p=R.nextInt(FILTER.length);
      String s=FILTER[p];
      qs.append(s);
    }
    String qss=qs.toString();
    int nArg=0;
    int posArg=0;
    Map<String,Object> argMap=new HashMap<>();
    while ((posArg=qss.indexOf("String_Node_Str",posArg)) >= 0) {
      posArg++;
      argMap.put("String_Node_Str" + nArg,nArg);
      nArg++;
    }
    try {
      q.setFilter(qss);
      if (argMap.isEmpty()) {
        q.execute();
      }
 else {
        q.executeWithMap(argMap);
      }
    }
 catch (    JDOUserException e) {
    }
catch (    NumberFormatException e) {
    }
catch (    Throwable e) {
      System.err.println("String_Node_Str" + qss);
      for (      String key : argMap.keySet()) {
        System.err.println("String_Node_Str" + key + "String_Node_Str"+ argMap.get(key));
      }
      System.out.println("String_Node_Str" + i);
      throw new RuntimeException(e);
    }
  }
  long t1=System.currentTimeMillis();
  System.out.println("String_Node_Str" + N_TEST);
  System.out.println("String_Node_Str" + (t1 - t0));
}