in reply to Encryption/Decryption with Perl and Java
I'll second sgifford's suggestion: First round-trip the encryption in one language. Then write the encryptor (or decryptor) in the other language and debug until you get the same output for the same input with both versions. Once you've debugged that, then you can encrypt the other half of the pair in the other language.
One additional thing I'll suggest: If you look up papers on the web for the encryption scheme you're interested in, you'll often find examples of plaintext, key and encrypted text. Using those examples you can (a) find your bugs more easily, and (b) ensure that you don't accidentally "debug" the wrong side of things. (I've done that before: My "debugged" version would encrypt and decrypt, but there was a bug that seriously compromised the integrity of the encoding scheme. Had I bothered to compare my encrypted text to the version in the paper, I'd've found the bug much sooner. Then maybe the junk version wouldn't have made it into production..... Blecch!)