FULL PRODUCT VERSION :
java version "1.6.0"
Java(TM) SE Runtime Environment (build 1.6.0-b105)
Java HotSpot(TM) Server VM (build 1.6.0-b105, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Linux host.domain 2.4.21-4.ELsmp #1 SMP Fri Oct 3 17:52:56 EDT 2003 i686 i686 i386 GNU/Linux

A DESCRIPTION OF THE PROBLEM :
Inserting a public key and a certicate chain failed.

This feature, which was wrintten for JDK1.4.2 and (source code mentioned below)is functioning perfect. When I decided to port to JDK1.6, it started throwing mentioned exception. (in the error message)

I downloaded the source code(JDK1.6) from your site, while verifying I found interesting as mentioned below.
-- java.security.Keystore.class
    public final void setKeyEntry(String alias, Key key, char[] password,
                                  Certificate[] chain)
        throws KeyStoreException
    {
        if (!initialized) {
            throw new KeyStoreException("Uninitialized keystore");
        }
        if ((key instanceof PrivateKey) &&
            (chain == null || chain.length == 0)) {
            throw new IllegalArgumentException("Private key must be "
                                               + "accompanied by certificate "
                                               + "chain");
        }
        keyStoreSpi.engineSetKeyEntry(alias, key, password, chain);
    }

It validates whether the key is privateKey and accompanied by certicate chain. Does that mean publicKey with certificate of chain permitted ? In my case it's valid as I am sending the Public key accompanied by certificate chain. As you see the keyStoreSpi which is an Interface to JavaKeyStore (below mentioned Class), engineSetKeyEntry mandate for the privateKey.

-- sun/security/provider/JavaKeyStore.class
    public void engineSetKeyEntry(String alias, Key key, char[] password,
                                  Certificate[] chain)
        throws KeyStoreException
    {
        KeyProtector keyProtector = null;

        if (!(key instanceof java.security.PrivateKey)) {
            throw new KeyStoreException("Cannot store non-PrivateKeys");
        }
 }


STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
1. Create a Ceriticate and a publickey
2. insert into keystore file $HOME/config/system.keystore
using the attached code. (Keystore type is "JKS")


EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Succefull insertion of the keyentry into the system.keystore file
ACTUAL -
The exceptions which is mentioned in the error message

ERROR MESSAGES/STACK TRACES THAT OCCUR :

Exception in thread "main" java.security.KeyStoreException: Cannot store non-PrivateKeys
at sun.security.provider.JavaKeyStore.engineSetKeyEntry(Unknown Source)
at java.security.KeyStore.setKeyEntry(Unknown Source)
at KeyStoreExample.encrypt(KeyStoreExample.java:89)
at KeyStoreExample.main(KeyStoreExample.java:39)

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
           java.security.KeyStore keyStore = java.security.KeyStore.getInstance("JKS");
                try {
                        java.io.FileInputStream ksStream = new java.io.FileInputStream(keyStoreFile);
                        keyStore.load(ksStream, password);
                }
                catch (java.io.FileNotFoundException ex) {
                }
                keyStore.load(null, password);
                java.security.cert.CertificateFactory certificateFactory = java.security.cert.CertificateFactory.getInstance("X.509");
                java.security.cert.Certificate cert = certificateFactory.generateCertificate(bCertificate);
                java.security.cert.Certificate[] certArr = new java.security.cert.Certificate[1];
                certArr[0] = cert;
                java.security.PublicKey pk = cert.getPublicKey();
                keyStore.setKeyEntry(alias, pk, password, certArr);
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
In my application (beta phase) I ignore the validation process to get around.