I'm having a nightmare with a clients CIS refund for his limited Company. I applied for the refund back in April using the online form requesting that the refund go towards paying the Company Corporation Tax. The refund was initially rejected because the figure I had requested didn't agree with HMRC's figures and they sent a download of what they held on their system for this client. I supplied bank statements, CIS statements and invoices as requested.
Roll on a few more months and the client is being debt chased for the Corporation Tax. A phone call chasing up the refund reveals that the final month of CIS in HMRC system is now showing a postive figure of deductions of £11k rather than a negative. So a £9.5k refund is now a £1.5k debt. I've been advised to correct this in my system Payroll Manager by doubling up the 11k to 22k as no one at HMRC can possibily have altered the figures after I sent them. I've also been asked to resend all the CIS reconciliation again as no one appears to have dealt with it. I know the figures in PAYE were correct when I sent the request for a refund I checked they matched up.
I'm reluctant to amend my figures in Payroll manager as they are correct, there are no positive CIS deduction figures. I'm worried that I'm fiddling the figures to correct HMRC system and in a few months HMRC will come back again and say its wrong.
Does anyone know if the excuse that HMRC keep trotting out of no one at HMRC can amend the PAYE/CIS figures is true or not? I can't see how the error has come from Payroll Manager.