The crypto function to get the SubjectKeyIdentifier from an X509Certificate has incorrect hard-coded assumptions about the size of the encoded information, meaning the calculation of the SKI from a 2048-bit RSA key is incorrect.
The method org.apache.ws.security.components.crypto.CryptoBase.getSKIBytesFromCert does not parse the DER encoding of information, but just tries to pick out the piece of the byte array that corresponds to the content of interest. However, that approach fails because the DER encoding is variable length, depending on the size of the data being encoded. e.g. a 1024-bit key in a DER BIT STRING takes 4 bytes header + 140 bytes data to encode, whereas a 2048-bit key takes 5 bytes header + 270 bytes data; the header is one byte longer for the larger key, so the data starts at a different point in the array.
To fix this, the DER data structures should be properly processed, reading the DER header bytes to determine the length of each data element (that also allows the generalization of handling any X.509 encoded public key, rather than just RSA keys as currently coded).
Attached is a suggested patch (against WSS4J 1.6.1) that implements this idea: it processes the SubjectPublicKeyInfo and SubjectKeyIdentifier DER-encoded byte arrays according to their ASN.1 definitions from RFC 3280/5280 to pick out the desired data bytes.