The following code reads and prints as expected with jdk6 1.6.0_22. But, this prints all zeros with jdk7 b119. This was run on Ubuntu 10.04.

File: Test.java

import java.io.*;

public class Test {
  public static void main(String[] args) throws Exception {
      InputStream is = Test.class.getResourceAsStream("Test.class");
      System.out.println(is);
      byte[] header = new byte[8];
      is.read(header);
      for (byte b : header) {
            System.out.println(b);
      }
      int minor = (header[4] << 8) | header[5];
      int major = (header[6] << 8) | header[7];
      System.out.println("minor " + minor);
      System.out.println("major " + major);
  }
}

Steps to reproduce:

1) java Test.java
2) jar cvf test.jar Test.class
3) java -cp test.jar Test

With jdk7, I got the following result:


$ ~/bin/jdk1.7.0/bin/java -cp test.jar Test
sun.net.www.protocol.jar.JarURLConnection$JarURLInputStream@117a8bd
-54
0
0
0
0
0
0
0
minor 0
major 0

With jdk6, I get the following result:

$ java -cp test.jar Test
sun.net.www.protocol.jar.JarURLConnection$JarURLInputStream@1690726
-54
-2
-70
-66
0
0
0
50
minor 0
major 50
If a println is added,

    System.out.println(is.read(header));

instead of

    is.read(header)

then the test works as expected even with jdk7 b119.

This does suggest it *may* be a JVM issue.