It seems that the Holiday Rent Payment problems are only affecting "registered" card payments, including those from booking.com.
We hope that when the errors are fixed you will be able to process these payments but we do not have a timescale for this. In the meantime the workaround is to send your guest a link to the online payment form or take payment over the phone.
We appreciate that it is inconvenient for the guest to re-enter their card details. But this method will secure payment.
You can find our help file on sending the payment link to guests here: http://help.supercontrol.co.uk/m/using-supercontrol/l/746578-how-do-i-send-a-guest-the-online-payment-link-for-their-booking