payrun calculating incorrect pension deduction

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I have just migrated to Sage Business Cloud Payroll and am trying to run the first payrun which is now overdue by a couple of days

We have one employee who is auto enrolled into a Pension scheme.

Business cloud is deducting an incorrect amount. The deduction should be 5% of the pensionable earnings, but sage is calculating 5% of the total earnings. 

All other employee deductions seem to be correct.

I have checked through all the relevant help articles and other answers on Sage City.  

Appreciate any help solving this issue.