I advise contacting our techs about this incomplete upgrade issue. Most likely it is caused by some wrong file/folder permissions issue. MCrypt usage was removed a long time ago. See https://www.x-payments.com/help/X-Payments:System_requirements_for_X-Payments_3:
mcrypt (Required only if upgrading X-Payments from a 3.0.x version; not needed if installing X-Payments version 3.1.0 or later. In 3.1.0 mcrypt has been replaced with openssl).
"Rijndael256" file is not a part of X-Payments anymore either.