FULL PRODUCT VERSION :
java version "1.6.0-rc"
Java(TM) SE Runtime Environment (build 1.6.0-rc-b104)
Java HotSpot(TM) 64-Bit Server VM (build 1.6.0-rc-b104, mixed mode)


ADDITIONAL OS VERSION INFORMATION :
SunOS 5.9 Generic_117171-11 sun4u sparc SUNW,Ultra-Enterprise
Linux 2.4.26-openmosix1mt2 #1 Mon Apr 18 15:32:52 MDT 2005 i686 i686 i386 GNU/Linux

A DESCRIPTION OF THE PROBLEM :
When trying to set the uncompressed size it does not save correctly.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Just replace the file to zip up with your own file and redirect the output to your own directory. When I take the test zip file and run zcat on it this is what I get for the header information.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Using file: /u/ramihu/test
Open /u/ramihu/sumTxt and zip it up...
Created the ZipEntry...
ZIP ENTRY SIZE: 2322595
File /u/ramihu/sumTxt zipped up and ready for read...
Attempting to get the uncompressed zip size: 2322595
Done using ZipInputStream for Information about the Zip entry. Trying ZipFile instead...
Using /u/ramihu/test for test.
Using a ZipEntry initialized through ZipFile.getName: /u/ramihu/sumTxt
Entry Size is: 2322595
ACTUAL -
Using file: /u/ramihu/test
Open /u/ramihu/sumTxt and zip it up...
Created the ZipEntry...
ZIP ENTRY SIZE: 2322595
File /u/ramihu/sumTxt zipped up and ready for read...
Attempting to get the uncompressed zip size: -1
Done using ZipInputStream for Information about the Zip entry. Trying ZipFile instead...
Using /u/ramihu/test for test.
Using a ZipEntry initialized through ZipFile.getName: /u/ramihu/sumTxt
Entry Size is: 2322595

******************* FROM THE COMMAND LINE ************************
telinux9{ramihu}38> file test
test: Zip archive data, at least v2.0 to extract
telinux9{ramihu}39> zcat -l test
         compressed uncompressed ratio uncompressed_name
             387872 -1 0.0% test
telinux9{ramihu}40>

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
package javatests;

import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.Enumeration;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
import java.util.zip.ZipInputStream;
import java.util.zip.ZipOutputStream;

public class Main {
    
    /** Creates a new instance of Main */
    public Main() {
    }
    
    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
        // TODO code application logic here
        byte[] buf = new byte[1024*8];
        
        try {
            File zipOut = new File( "/u/ramihu/test" );
// File zipOut = new File( "/u/summary/DEVL/sums/BDB/8Q/4B/11UNH" );
            System.out.println( "Using file: " + zipOut.toString() );
            File sourceFile = new File( "/u/ramihu/sumTxt" );
            BufferedOutputStream fileBuf = new BufferedOutputStream( new FileOutputStream( zipOut ) );
            
            System.out.println("Open " + sourceFile.toString() + " and zip it up...");
            
            // Create the ZIP file
            ZipOutputStream out = new ZipOutputStream( fileBuf );
            
            // Compress the files
            FileInputStream in = new FileInputStream( sourceFile );
            
            ZipEntry ze = new ZipEntry( sourceFile.toString() );
            ze.setSize( sourceFile.length() );
            ze.setTime( sourceFile.lastModified() );
            System.out.println( "Created the ZipEntry..." );
            System.out.println("ZIP ENTRY SIZE: " + ze.getSize() );
            // Add ZIP entry to output stream.
            out.putNextEntry(ze);
            
            // Transfer bytes from the file to the ZIP file
            int len;
            while ((len = in.read(buf)) > 0) {
                out.write(buf, 0, len);
            }
            
            // Complete the entry
            
            out.closeEntry();
            in.close();
            
            out.finish();
            out.flush();
            
            // Complete the ZIP file
            out.close();
            
            System.out.println( "File " + sourceFile.toString() + " zipped up and ready for read..." );
            
            // Now open it back up and check the data.
            ZipInputStream in1 = new ZipInputStream(new FileInputStream(zipOut));
            
            // Get the first entry
            ZipEntry entry = in1.getNextEntry();
            System.out.println("Attempting to get the uncompressed zip size: " + entry.getSize());
            
            // Close the streams
            in1.close();
            System.out.println( "Done using ZipInputStream for Information about the Zip entry. Trying ZipFile instead..." );
            
            try {
                // Open the ZIP file
                ZipFile zf = new ZipFile(zipOut);
                
                System.out.println( "Using " + zipOut.toString() + " for test.");
                
                // Enumerate each entry
                for (Enumeration entries = zf.entries(); entries.hasMoreElements();) {
                    // Get the entry name
                    ZipEntry ent = ((ZipEntry)entries.nextElement());
                    System.out.println( "Using a ZipEntry initialized through ZipFile.getName: " + ent.getName() );
                    System.out.println( "Entry Size is: " + ent.getSize() );
                }
            } catch (IOException e) {
                e.printStackTrace();
            }
            
        } catch (IOException e) {
            // Need to throw some kind of an error here...
            e.printStackTrace();
        }
    }
}
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Yes, make a system call to your platform zip and do it that way.