Java Security

I'm trying to validate an X509 certificate but I keep getting "No key found!" and "cannot find validation key" errors.
I generate the certificate and put it in a keystore with the following code:

//Es genera la parella de claus i el certificat X.509
        CertAndKeyGen claus = new sun.security.x509.CertAndKeyGen("RSA", "MD5WithRSA" );
        X500Name x500Name = new sun.security.x509.X500Name(CN,OU,O,L,ST,C);
        claus.generate( 512 );
        X509Certificate[] cadena = new X509Certificate[1];
        cadena[0] = claus.getSelfCertificate(x500Name, 24*60*60);

        //Es crea el KeyStore per guardar les claus
        KeyStore ks = KeyStore.getInstance("JKS");
        ks.load(null, null);
        ks.setKeyEntry("Alias", claus.getPrivateKey(), "ContrasenyaPrivada".toCharArray(), cadena);
        
        //Es guarda el KeyStore a un fitxer amb extensi� .ks
        FileOutputStream fos = new FileOutputStream("fitxerclaus.ks");
        ks.store(fos, "ContrasenyaFitxer".toCharArray());
        fos.close();

But the certificate format seems to be correct since I've also tried generating an X509 certificate with KeyTool and the validation still fails.
I don't know wether this is due to the X509KeySelector I'm using (taken from http://java.sun.com/developer/technicalArticles/xml/dig_signature_api/index.html) or because of the format of my XML file. I've even created a new project copying the exact same code from the mentioned link and generating the XML file with this code

	// Create the Document that will hold the resulting XMLSignature
	DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
	dbf.setNamespaceAware(true); // must be set
	Document doc = dbf.newDocumentBuilder().newDocument();

(I use JDOM and then convert it to DOM) but validation still doesn't work. I've spent 2 days trying to figure out how to solve this problem but I can't seem to do it so if anyone can help me it would be be much appreciated.