I see you are using self-installed download-able X-Payments as we do not have such issues with hosted X-Payments plans.
What payment processor are you using? This may be similar to a problem explained at http://help.x-cart.com/index.php?title=X-Payments:User_manual#CyberSource_Internal_Error
i.e. some security or key file needed for a payment integration is not readable by web server daemon on your server.