CSP (Type:80) v4.0.9018 KC1 Release Ver:4.0.9953 OS:Linux CPU:IA32 FastCode:READY:AVX.

    public static void main(String[] args) throws Exception {

        String alias = "test";
        String dn = "CN=Margarita";
        String alg = JCP.GOST_EL_SIGN_NAME;

        KeyStore keyStore = KeyStore.getInstance(JCSP.HD_STORE_NAME, JCSP.PROVIDER_NAME);
        keyStore.load(null, null);

        KeyPairGenerator kpg = KeyPairGenerator.getInstance(JCP.GOST_EL_DEGREE_NAME, JCSP.PROVIDER_NAME);
        KeyPair kp = kpg.generateKeyPair();

        // самоподписанный

        GostCertificateRequest request = new GostCertificateRequest(JCSP.PROVIDER_NAME);
        byte[] selfCertEncoded = request.getEncodedSelfCert(kp, dn, alg);

        CertificateFactory factory = CertificateFactory.getInstance("X.509");
        X509Certificate selfCert = (X509Certificate) factory.generateCertificate(new ByteArrayInputStream(selfCertEncoded));

        JCPProtectionParameter parameter = new JCPProtectionParameter("123".toCharArray());
        JCPPrivateKeyEntry entry = new JCPPrivateKeyEntry(kp.getPrivate(), new Certificate[] {selfCert});

        // сохраняем заглушку и ключ

        keyStore.setEntry(alias, entry, parameter);
        System.out.println("OK-1");

        // выпускаем сертификат в УЦ

        request = new GostCertificateRequest(JCSP.PROVIDER_NAME);

        int keyUsage =
            GostCertificateRequest.DIGITAL_SIGNATURE |
            GostCertificateRequest.NON_REPUDIATION;

        request.setKeyUsage(keyUsage);
        request.addExtKeyUsage(GostCertificateRequest.INTS_PKIX_EMAIL_PROTECTION);

        request.setPublicKeyInfo(kp.getPublic());
        request.setSubjectInfo(dn);

        request.encodeAndSign(kp.getPrivate(), alg);
        byte[] certEncoded = request.getEncodedCert("http://www.cryptopro.ru/certsrv/");

        // устанавливаем 2 раза!

        X509Certificate cert = (X509Certificate) factory
            .generateCertificate(new ByteArrayInputStream(certEncoded));

        keyStore.setCertificateEntry(alias, cert);
        System.out.println("OK-2");

        keyStore.setCertificateEntry(alias, cert); // еще раз
        System.out.println("OK-3");

    }