Thank you for contacting us for ezPaycheck payroll software . I think the 401K deduction set up caused this issue.

Please open the set up screen of 401K deduction, uncheck the option "exempt from federal and state income tax" for 401K deduction and save the change. When you add a new check, both ezPaycheck and QuickBooks will have the same amount.

You can also learn more by clicking this link:

How to handle pre-tax and after-tax deductions
http://www.halfpricesoft...ck-Payroll-software.aspx 

Please try it.

Thank you.

Casey

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Problem; a VA employee is paid biweekly, yearly salary is $200,000.00, Federal tax setup: married, 0 exemptions, extra withholding $1,200.00, and extra state withholding $280.00 with 0 exemptions. THE FEDERAL TAX IS: FOR Quick Books: $2763.00 and Ez is: $2504.20. The State tax withheld is: Quick Books: $706.00 and EZ is $652.60. Why? One other piece of info 401K is a Roth and $924.62 is withheld each paycheck.

stanley