What is the difference between SHA256WITHRSA and SHA256WITHRSAENCRYPTION digest algorithms?
It seems that djigzo uses bouncycastle and if you look in the source at the DefaultSignatureAlgorithmIdentifierFinder, e.g., here, then you find:

algorithms.put("SHA256WITHRSAENCRYPTION", PKCSObjectIdentifiers.sha256WithRSAEncryption);
algorithms.put("SHA256WITHRSA", PKCSObjectIdentifiers.sha256WithRSAEncryption);


Thus, it seems that both refer to sha256WithRSAEncryption, which means RSA with SHA-256 and PKCS #1 v1.5 padding.