Java Security

I am trying to pass some encrypted information as a cookie; a Perl program will read this cookie and decrypt it. I can get an encryption/decryption scheme to work in Java, as long as I leave the encrypted part as a byte. If I convert it to a string (to print to a file, say) and then try to convert that back to a byte and decrypt it, I have no success.

At least, that's what I think is happening. I am using Blowfish in CBC mode and PKCS5 padding (this is at the request of Perl). I am also doing an MD5 hash on the key before I use it. Is there something going on in terms of type conversion when I encrypt/decrypt a file that I'm not aware of?

Thanks!