Estou usando o java.security.KeyPairGenerator para gerar um par de chaves RSA e, em seguida, tentar carregar a chave privada por meio da classe KeyPair fornecida no Jsch (0.1.49). O código:

public static void main(String[] args) {
    String header = "-----BEGIN RSA PRIVATE KEY-----";
    String footer = "-----END RSA PRIVATE KEY-----";
    KeyPairGenerator keyPairGenerator;
    try {
        keyPairGenerator = KeyPairGenerator.getInstance("RSA");
        keyPairGenerator.initialize(2048, new SecureRandom());
        PrivateKey privateKey = keyPairGenerator.genKeyPair().getPrivate();
        String key = new String(Base64.encodeBase64(privateKey.getEncoded()));
        StringBuffer pem = new StringBuffer(header+"\n");
        int len=key.length();
        for( int idx=0 ; idx < len ; idx+= 64 )
            pem.append(key.substring(idx, (idx+64)<len?(idx+64):len)+"\n");
        pem.append(footer);
        String privateKeyStr = pem.toString();
        System.out.println(privateKeyStr);
        com.jcraft.jsch.KeyPair.load(null, privateKeyStr.getBytes(), null);
    } catch (JSchException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (NoSuchAlgorithmException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
}

A saída por System.out:

-----BEGIN RSA PRIVATE KEY-----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-----END RSA PRIVATE KEY-----

Então eu vejo exceções do KeyPair dizendo que é uma chave privada inválida, eu verifiquei o código-fonte do JSch, a exceção é devido a umaÍndice fora dos limites enquanto os dados estão sendo analisados. O stacktrace:

com.jcraft.jsch.JSchException: invalid privatekey: [B@5f2e5f2e
    at com.jcraft.jsch.KeyPair.load(KeyPair.java:809)
    at com.ibm.maestro.common.utils.Test.main(Test.java:149)

Eu estou supondo que eu possa corrigir esse problema, adicionando / alterando algumas parms ao gerar o par de chaves, qualquer pista? Sua ajuda será muito apreciada!