Amount Overdue Notice Issued for SA Late Payment, yet Tax has been paid!!

What do I do? The payment has gone to Shipley with my Tax code as reference for the right amount, same as it does every year with no issues, but this year I have been told it has not been paid!! I can see it has left my account to HMRC Shipley on 31st January - how on earth do I resolve this? I'm worried sick that every day I will be accruing more interest and will fail to get hold of anybody to tell them! Very very stressed about this.

Hi Helen Flack,
We are sorry to hear of the stress this has caused you.
If your payment hasn't reached your account yet, we should be able to trace and allocate it.
Please contact us by webchat or phone here to allow us to do this.
Self Assessment: general enquiries
Thank you. 

Same happened to me. Paid it on 29 Jan and it appeared as paid in my Tax Account. They sent a letter on 7 Feb. Best way to contact them was webchat with a human. They didn't know why it was sent or admit it was an error. My wife got a letter too when she was on a direct debit started in December that was correctly paying into her account. Have they sent 1000s out in error? we wonder.