Try dumping password as bytes in both cases.

Perhaps you are using some exotic character that is getting translated
to byte differently in each case.

--
Canadian Mind Products, Roedy Green.
Coaching, problem solving, economical contract programming.
See http://mindprod.com/jgloss/jgloss.html for The Java Glossary.

just to be sure, make this minor mod to your program:

import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.math.BigInteger;

public class MD5Test
  {
  /**
   * test MD5 digest
   *
   * @param args not used
   */
  public static void main ( String[] args )
     {

     try
        {
        String password = "foo";
        MessageDigest md = MessageDigest.getInstance( "MD5" );
        md.update( password.getBytes( "8859_1" ) );
        BigInteger hash = new BigInteger( 1, md.digest() );
        String hpassword = hash.toString( 16 );
        System.out.println(hpassword);
        }

     catch ( NoSuchAlgorithmException ns )
        {
        ns.printStackTrace();
        }
     }
  }

--
Canadian Mind Products, Roedy Green.
Coaching, problem solving, economical contract programming.
See http://mindprod.com/jgloss/jgloss.html for The Java Glossary.

D3 B0 73 84 D1 13 ED EC 49 EA A6 23 8A D5 FF 00
is a MD5 hash of  "foo<lf>"
so your Linux implementation is simply adding an extra 0x0A byte
to the data that actually gets hashed.

Here is a useful tool I wrote to quickly sort out these types of problems,
including issues with UNICODE encoded data:
  http://www.jensign.com/JavaScience/www/messagedigest

(there is a JavaPlugin version of above, but the signature verification fails due to
some "leaf" verification issues introduced in later versions of 1.4.x

- Mitch Gallant

<snip>

The file containing "foo" that you're running md5sum against has a
carriage return at the end.  Change the code to:

String password = "foo\n";

and it prints:

d3b07384d113edec49eaa6238ad5ff00

  This is indeed the MD5 hash of "foo".

  The MD5 hash of "foo\n" is D3B07384 D113EDEC 49EAA623 8AD5FF00.
If you did something like

   echo foo|md5sum

then try something like

   echo -n foo|md5sum

--Mike Amling