UK Sage 200 CIS

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My company moved from Sage 50 to Sage 200 before I joined and apparently there were no issues with the CIS module on Sage 50. However in reconciling the last year's accounts I have discovered a number of variances between the CIS labour value entered re the purchase ledger invoice and the value submitted to HMRC on the monthly CIS return. Investigation by our support provider has shown this to be caused by the way the invoices, credit notes and payments on the purchase ledger accounts were allocated. I have been assured that the team have not changed their methods.
Has anyone else come across this issue, and if so, how can it be dealt with?
 

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