From version 9 or 10 to version 11 was a big change for payroll and not everything could be converted automatically. The was a finish payroll conversion step for payroll before you could use the payroll module in version 11. There was a step during this process where it asked you to confirm how employer liability items were to be treated.
There will be a maintenance release in the next few weeks to change the 941 report to the updated social security amounts.
Wrong Federal Withholding Deducts
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