Problema com waitFor() + pdftohtml no Linux

//verifica se retornou erros
        stream = new StreamHandler( process.getErrorStream() , "ERRO", area);
        //verifica se teve output
        streamOut = new StreamHandler( process.getInputStream() , "SAÍDA", area);
        Thread tStream = new Thread( stream );
        Thread tStreamOut = new Thread( streamOut );

        tStream.start();
        tStreamOut.start();

        try {
            int exitVal = process.waitFor();
            area.append( "Processo encerrou com status: " );
            area.append( exitVal + "\n" );
        } catch (InterruptedException ex) {}


        stream.stopHeader(true);
        streamOut.stopHeader(true);

public class StreamHandler implements Runnable {

    InputStream is;
    String type;
    JTextArea txtMsg;
    private boolean stopHandler;

    public StreamHandler( InputStream is, String type,  JTextArea txtMsg) {
        this.is = is;
        this.type = type;
        stopHandler = false;
        this.txtMsg = txtMsg;
    }

    public void run() {
        while( !stopHandler ) {
            try {
                InputStreamReader isr = new InputStreamReader(is);
                BufferedReader br = new BufferedReader(isr);
                String line = null;
                while ((line = br.readLine()) != null) {
                    System.out.println( type + ">>" + line + "\n" );
                    txtMsg.append(type + ">>" + line + "\n");
                }
            } catch (IOException ioe) {
                ioe.printStackTrace();
            }    
        }
    }

    public void stopHeader( boolean stop ) {
        this.stopHandler = stop;
    }
}

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.text.SimpleDateFormat;
import java.util.Date;

import javax.swing.JOptionPane;

public class TesteComBAT{
	public static String timeFormat = "HH:mm:ss"; 
	public static SimpleDateFormat formata;
	private static final String CAMINHO_PADRAO = "C:\\Arquiv~1\\XXX\\XXXXXX\\XXXXX\\"; // <- caminho do BAT
	
	public static void main(String[] args) {
		formata = new SimpleDateFormat(timeFormat);
		final String inicio = formata.format(new Date());
		try {
		      String line;
		      Process p = Runtime.getRuntime().exec(CAMINHO_PADRAO + "MEU_PROCESSO.bat");
		      BufferedReader input =new BufferedReader(new InputStreamReader(p.getInputStream()));
		      while ((line = input.readLine()) != null) {
		        System.out.println(line);
		      }
		      input.close();
			  JOptionPane.showMessageDialog(null, "Inicio -> " + inicio + " \n Fim -> " + formata.format(new Date()));
		} catch (IOException e) {
			e.printStackTrace();   
		} 
	}
}