My mutt/PGP config stopped working in the 6.4 release. I was unable to open encrypted mail sent to me. In case it saves anyone some trouble, I am sharing a workaround I have found:
There's a new mutt option called pgp_check_gpg_decrypt_status_fd which is set to 'yes' by default. When set, mutt will try to find lines which begin with the string "[GNUPG:]" in gpg's output. No such lines are found in my case. If mutt does not see such lines, it will believe decryption has failed, and not display the messsage even though it was in fact decrypted correctly. Setting this option to 'no' made my setup work again.