If your one-off paycheck was for your normal net paycheck amount, then all your W-2 boxes should be higher than your year-end pay stub. Even if the one-off paycheck was for your normal gross pay (before all withholdings), all the boxes on your W-2 should be grossed up. Your employer is required to withhold payroll taxes from any monies you receive as employee compensation and would have paid those taxes along with the rest of the Q1 withholdings.
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