Yes I'm dealing with a similar case, where the computer didn't pick up the manual payments until several months later, thus creating an overpayment. We have challenged the overpayment in the usual way, and are still awaiting a response.
The point you make about the 'off system payment declaration' is interesting and potentially problematic. I will have to find out whether my client signed any such document.
During a phone call to HMRC they said that a lot of overpayments are caused this way, becuase the computer system never picks up that manual payments have been made until some time later. The declaration you have referred to would appear to reflect a recognition of this problem on the part of HMRC, and a clear attempt to try and secure recovery of the resulting overpayments. This is pretty rough on the poor punter when the blame lies squarely on the shoulders of the revenue. Surely the HMRC should instead be focusing their attention on changing their procedures to make sure that manual payments are promptly recorded?
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