X-Payments does work. There won't be any need to re-certify X-Payments.
The "Mastercard issue" is related to
LUHN verification of Mastercard card numbers. For some reason it doesn't "like" some Mastercards issued by some banks. X-Cart uses the same algo as well as some other e-commerce solutions.
Devs are figuring out the reason, but the quick fix is to make checking card numbers optional (I'll follow up with the patch shortly - applying it doesn't change the PA-DSS part of X-Payments so no re-certification is required).