JVM died by SIGSEGV at ZipFile.getEntry.  
Stack: [0xffff80ffb296e000,0xffff80ffb2a6e000],  sp=0xffff80ffb2a6b078,  free space=1012k 
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) 
C  [libc.so.1+0x8d4fe]  memcpy+0x135e C  [libzip.so+0xe121]  ZIP_GetEntry+0x91 
C  [libzip.so+0x4ef1]  Java_java_util_zip_ZipFile_getEntry+0xa1 J  java.util.zip.ZipFile.getEntry(JLjava/lang/String;Z)J  


testcase present 
The java sources are in testcase.tar. 
CrashTest.java is very simple: 
======================================================= 
package mypkg1; 

import java.io.IOException; 
public class CrashTest { 
public static boolean loadClass(String cname) { 
    try { 
            System.out.println("loading class :" + cname); 
            Class.forName(cname); 
            System.out.println("loading class :" + cname + " done."); 
            return(true); 
    } catch (ClassNotFoundException e) { 
      System.out.println("failed to load class '" + cname + "': " + e); 
    } return(false); 
}  

/** 
  * param args 
  */ 
public static void main(String[] args) { 
    if (! loadClass("mypkg2.MyClass1")) { 
       System.out.println("loadClass failed.");  
       return; 
    } 
    System.out.println("Press enter to continue..."); 
    try {  
        System.in.read();  
    } catch (IOException e) { 
        return; 
    }  
    if (! loadClass("mypkg2.MyClass2")) { 
       System.out.println("loadClass failed."); 
       return; 
    } 
    System.out.println("main done"); 
 } 
} 

 ======================================================= 
This program does:
 load mypkg2.MyClass1
 wait for keyboard input
 load mypkg2.MyClass2

mypkg2.MyClass1 and mypkg2.MyClass2 are in mypkg2_v1.jar and mypkg2_v2.jar:
=======================================================
# jar tvf mypkg2_v1.jar
     0 Mon Sep 02 09:45:30 KST 2013 META-INF/
    71 Mon Sep 02 09:45:30 KST 2013 META-INF/MANIFEST.MF
   681 Mon Sep 02 09:45:30 KST 2013 mypkg2/MyClass1.class
   681 Mon Sep 02 09:45:30 KST 2013 mypkg2/MyClass2.class
# jar tvf mypkg2_v2.jar
     0 Mon Sep 02 09:45:30 KST 2013 META-INF/
    71 Mon Sep 02 09:45:30 KST 2013 META-INF/MANIFEST.MF
   734 Mon Sep 02 09:45:30 KST 2013 mypkg2/MyClass1.class
   734 Mon Sep 02 09:45:30 KST 2013 mypkg2/MyClass2.class
=======================================================

If CrashTest is run without changing the jar file (ie. if you skip step 3)
there is no problem.