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You need to have your employer issue you corrected W-2's (Form W-2c) for the years that are in error. Then you will need to file an amended tax return for each tax year to report the corrected W-2. Amended tax returns with a tax refund can currently only be filed for tax years 2020, 2021 and 2022.
It's not clear what you mean by "my end of year checks" and "my end of year pay." You can't compare the gross pay on your W-2 to the net pay that you actually receive in your paychecks. The wages in box 1 of your W-2 are your gross pay, before any deductions. The amount of your paycheck is the net amount that's left after all the deductions. Ask your employer to explain the difference between the gross amount on your W-2 and the net amount that you received. Some of the things that could be deducted from your gross pay include the following.
If you are a tipped employee, your W-2 box 1 wages will include your tips.
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