This has been asked a couple of times, but none provide coded test cases. Here I give an example of the problem:
- programmatic generation of a Keystore (works)
 - creation of certificate within that store (works)
 - saving keystore to disk (works)
 - listing keystore with keytool (works)
 - loading the keystore programmatically (fails with IOException: InvalidKeystoreFormat)
 
What I dont get is that in both save and load, I use KeyStore.getInstance("JKS"), but its failing. Any suggestions welcome!
Runtime output:
Creating private keystore at 'private.keystore'. Created keystore, now created signer cert Created signer cert, saving cert Reloading keystore: Failed to load the keystore after creation: Invalid keystore format
Test case source:
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.security.InvalidKeyException;
import java.security.KeyStore;
import java.security.KeyStoreException;
import java.security.NoSuchAlgorithmException;
import java.security.NoSuchProviderException;
import java.security.PrivateKey;
import java.security.SignatureException;
import java.security.cert.Certificate;
import java.security.cert.CertificateException;
import java.security.cert.X509Certificate;
import sun.security.x509.X500Name;
public class KeystoreCreator
{
 private String fPrivateKeyStore;
 private String fPrivateKeyStorePassword;
 private String fPrivateKeyStoreKeyPassword;
 private String fPublicKeyCipherPassword;
 private String fPrivateKeyAlias;
 /**
  * @param args
  * @throws Exception 
  */
 public static void main(String[] args) throws Exception
 {
  KeystoreCreator creator = new KeystoreCreator();
  creator.setPrivateKeyStore("private.keystore");
  creator.setPrivateKeyStorePassword("beer123");
  creator.setPrivateKeyAlias("myalias");
  creator.setPrivateKeyStoreKeyPassword("beer123");
  creator.setPublicKeyCipherPassword("beer123");
  creator.initKeyStores();
 }
 public KeystoreCreator()
 {  
 }
 public void setPrivateKeyStore(String name)
 {
  fPrivateKeyStore=name;
 }
 public void setPrivateKeyStorePassword(String pass)
 {
  fPrivateKeyStorePassword=pass;
 }
 public void setPrivateKeyStoreKeyPassword(String pass)
 {
  fPrivateKeyStoreKeyPassword=pass;
 }
 public void setPublicKeyCipherPassword(String pass)
 {
  fPublicKeyCipherPassword=pass;
 }
 public void setPrivateKeyAlias(String alias)
 {
  fPrivateKeyAlias=alias;
 }
    public void initKeyStores() throws Exception
    {
        OutputStream out = null;
        File f=new File(fPrivateKeyStore);
        if (f.exists())
        {
         f.delete();
         if (f.exists())
         {
          throw new IOException("Want to remove the keystore but can't, still reported as present after removal");
         }
        }
        try
        {
         System.out.println("Creating private keystore at '" + fPrivateKeyStore + "'.");
         out = new FileOutputStream(fPrivateKeyStore);
         KeyStore privateKeyStore = KeyStore.getInstance("JKS");
         privateKeyStore.load(null, fPrivateKeyStorePassword.toCharArray());
         System.out.println("Created keystore, now created signer cert");
         X500Name x500name=getCA();
         Certificate cert = createCertificate(fPrivateKeyAlias, fPrivateKeyStoreKeyPassword, x500name, privateKeyStore);
         System.out.println("Created signer cert, saving cert");
         privateKeyStore.store(out, fPublicKeyCipherPassword.toCharArray());
         out.flush();
         out.close();
         //try to load it.
         KeyStore reloadedKeyStore = KeyStore.getInstance("JKS");
         try
         {
          InputStream reloadedIs=getClass().getClassLoader().getResourceAsStream(fPrivateKeyStore);
          if (reloadedIs!=null)
          {
           System.out.println("Reloading keystore:");
           reloadedKeyStore.load(reloadedIs, fPrivateKeyStorePassword.toCharArray());
          }
         }
         catch (Exception e)
         {
          System.err.println("Failed to load the keystore after creation: "+e.getLocalizedMessage());
         }
        }
        catch (Exception e)
        {
         System.err.println("Failed to save the keystore: "+e.getLocalizedMessage());
        }
    }
    private X500Name getCA() throws IOException
    {
     return new sun.security.x509.X500Name("a","b", "c","d","e", "GB");
    }
    public Certificate createCertificate( String alias, String keyPassword,
            sun.security.x509.X500Name x500Name, KeyStore keyStore ) throws NoSuchAlgorithmException,
            InvalidKeyException, CertificateException, SignatureException, NoSuchProviderException,
            KeyStoreException {     
        sun.security.x509.CertAndKeyGen keypair = new sun.security.x509.CertAndKeyGen( "RSA", "MD5WithRSA" );
        keypair.generate( 1024 );
        PrivateKey privKey = keypair.getPrivateKey();
        X509Certificate[] chain = new X509Certificate[1];
        chain[0] = keypair.getSelfCertificate( x500Name, 7000 * 24 * 60 * 60 );
        keyStore.setKeyEntry( alias, privKey, keyPassword.toCharArray(), chain );
        Certificate cert = keyStore.getCertificate( alias );
        return cert;
    }
}