Test:
import java.security.KeyStore;
import java.security.KeyStoreException;
import java.security.SecureRandom;
import java.util.Enumeration;

import sun.security.tools.keytool.CertAndKeyGen;
import sun.security.x509.X500Name;

public class WinKeyStoreTest {

    public static void main(String[] args) throws Exception {
        KeyStore keyStore = KeyStore.getInstance("Windows-MY");
        keyStore.load(null, null);
        System.out.println("keystore loaded");
        listAlias(keyStore);

        String alias = "test";
        int number = 2;

        System.out.println("add alias...");
        CertAndKeyGen ckg = new CertAndKeyGen("RSA", "SHA1withRSA");
        ckg.setRandom(new SecureRandom());
        for (int i = 0; i < number; i++) {
            ckg.generate(1024);
            keyStore.setCertificateEntry(alias,
                    ckg.getSelfCertificate(new X500Name("CN=TEST"), 1000));
        }
        System.out.println("alias added");
        listAlias(keyStore);

        keyStore.load(null, null);
        System.out.println("keystore reloaded");
        listAlias(keyStore);
    }

    private static void listAlias(KeyStore keyStore) throws KeyStoreException {
        System.out.println("===== alias list =====");
        for (Enumeration<String> e = keyStore.aliases(); e.hasMoreElements();) {
            String alias = e.nextElement();
            System.out.println(alias);
        }
        System.out.println("======================");
    }
}

Test output:
keystore loaded
===== alias list =====
======================
add alias...
alias added
===== alias list =====
test
======================
keystore reloaded
===== alias list =====
test
test (1)
======================

The test adds two entries with the same alias to Windows-MY keystore, before reload the keystore, it lists only one alias.