You are running PRREPORT from your Payroll Records report with the correct Pay Period Begin and End Dates set with the same Regular Earnings suffix and Account Suffixes?
I wonder if you have duplicate check numbers in your Accrued Wages ledger? Issue /Document View XR (closed by reconcile) in the employees accrued wages ledger and match the timecards to the payments. Any descrepancies?
Is there a manual entry in the employees ~REG account that doesn’t appear in the accrued wages ledger? Go to the employee regular earnings account and issue /Go Item and type the check date you got with PRREPORT.
Running Check Books might be a good thing to do if there is damage in the books.