Payroll Calculation - Vehicle Allowance

I have recently taken over as Controller for a small General Contracting firm.  

The previous Controller was using Paychex as a payroll processor but It's just been a nightmare so I have decided to bring payroll back in-house.  I'm finding some issues though with Paychex and the setup of our calculations.  

1. The OQ (I'm in Oregon) is not calculating the PFML correctly and Paychex is showing that we've had excess wages in 2023 when we have not. 

2. We have a "Vehicle Allowance" calculation.  To my knowledge this should be a taxable calculation and it APPEARS to be set up properly but it doesn't seem to be showing up in the "taxable wages". 

I'd really rather not back out all of the payrolls for the year to get the balances fixed and wonder if anyone has any idea about the best way to accomplish getting my reports to show up properly so that I can amend my 941's and OQ.  

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