In a case where a taxpayer has PAYE income, and is subject to self-assessment, if a coded underpayment exceeds the tax paid at source via PAYE, the HMRC tax calculation is restricting the underpayment coded to the tax paid at source, resulting in their calculation showing less tax due.
EG. Underpayment coded £1,000. Tax paid via PAYE, £800. SA tax payable £1,500. HMRC will calculate SA tax payable to be £1,300. This has a knock on effect to POAs. I've spoken to HMRC who confirm that their calculation is doing this, and I've spoken to IRIS who confirm that their calculation is per HMRC specifications. I believe that IRIS are correct.
I have no idea who to talk to next. Perhaps @John Hemming has a clue who to talk to?