"Windows-MY" Keystore won't list all available aliases

Question

I have a problem listing all available certificates installed in my personal (windows) keystore.

I use following code to get a list of all certificate aliases:

public static void main(String[] args) {
    try {
        KeyStore ks = KeyStore.getInstance("Windows-MY");
        ks.load(null, null);
        Enumeration<String> en = ks.aliases();

        while (en.hasMoreElements()) {
            String aliasKey = (String) en.nextElement();

            System.out.println("---> alias '" + aliasKey + "'");
            //TODO GET CERT ETC 
        }

    } catch (Exception ioe) {
        System.err.println(ioe.getMessage());
    }
}

It works fine, listing 2 of my recently installed certificates.

HOWEVER.

After a computer restart, code lists only one certificate alias, though in system (using certmgr.msc) i still have two certificates active.

Whats more - installed certificates are from smartcards: - ENCARD (with ENIGMA CAPI) - UNIZETO CARD (dont know details)

Problem seems to occur, when i use ENCARD with API. After restart, UNIZETO card still works fine.

Any ideas?