I have modified the code to include some checks:
public class Laj {
  private static void printLines(String name, InputStream ins) throws Exception {
    String line = null;
    BufferedReader in = new BufferedReader(
        new InputStreamReader(ins));
    while ((line = in.readLine()) != null) {
        System.out.println(name + " " + line);
    }
  }
  private static void runProcess(String command) throws Exception {
    Process pro = Runtime.getRuntime().exec(command);
    printLines(command + " stdout:", pro.getInputStream());
    printLines(command + " stderr:", pro.getErrorStream());
    pro.waitFor();
    System.out.println(command + " exitValue() " + pro.exitValue());
  }
  public static void main(String[] args) {
    try {
      runProcess("javac Main.java");
      runProcess("java Main");
    } catch (Exception e) {
      e.printStackTrace();
    }
  }
}
Here is the Main.java:
public class Main {
  public static void main(String[] args) {
    System.out.println("ok");
  }
}
When everything is fine, it just works:
alqualos@ubuntu:~/tmp$ java Laj
javac Main.java exitValue() 0
java Main stdout: ok
java Main exitValue() 0
Now, for example, if I have some error in Main.java:
alqualos@ubuntu:~/tmp$ java Laj
javac Main.java stderr: Main.java:3: package Systems does not exist
javac Main.java stderr:     Systems.out.println("ok");
javac Main.java stderr:            ^
javac Main.java stderr: 1 error
javac Main.java exitValue() 1
java Main stdout: ok
java Main exitValue() 0
It still prints "ok" because the previously compiled Main.class is still there, but at least you can see what exactly is happening when your processes are running.
     
    
Process.getOutputStream?exitValue()'s of the processes? What do they output in ErrorStreams?