I think you have resolved this now. The HMRC staff dealing with this appear to be unaware of how their own systems work.
Gift Aid is added to the PAYE system as a net figure whilst personal pension relief (a relief at source payment) has to be grossed up first.
Presumably having both things to enter has confused the operator and they have added both as net figured in error.
You can refer them to their own guidance - link below -and ask for the correct PPR to be included in the calculation.
I don't know whether that on its own is sufficient to bring back the Marriage Allowance but it is at least a starting point where there will presumably no longer be any higher rate liability.
https://www.gov.uk/hmrc-internal-manuals/paye-manual/paye130025
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