Tax variation on car allowances

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Tax variation on car allowances

I have a situation where I have followed the MYOB instructions in setting up a PAYG variation for a car allowance however the way it is set up does not appear to be STP compliant.  The way it is set up is by exempting the car allowance from PAYG withholding then adding a deduction for the new % rate but the deduction cannot be given the ATO reporting category of PAYG withholding.  The current away around it is by manually overriding the PAYG withholding amount every pay cycle for each employee with a PAYG variation.  Can this please be looked into, surely I am not the only one in this situation.

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