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Hi toniw-penfoldpro,
If an employee's payroll tax configuration has been changed the changes made will apply for any future pay runs only. I would recommend also checking the Tax file declaration (TFD) set up since taxes is also calculated based on the employees TFD, pay schedule and gross earnings. Here's how:
When you create your pay runs there should be taxes calculated on them. For your reference you can check this link to learn more about: Update employee tax file declaration information for STP Phase 2.
Feel free to post again in the Community if you have further concerns. I'll be here to help you.
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