If the paychecks were created while QuickBooks was not calculating taxes, then the taxes on those checks are each set to 'manual override' mode, and they won't calculate.
Assuming you didn't already create the paychecks, but you started the process and entered time and that sort of thing, you can resume the payroll run and then right click on each employee who has a yellow background, meaning the paycheck is pending (and the taxes are set to 'manual override'), and choose Revert Paycheck. Then the taxes will calculate as expected.
However, this will also reset any work you have applied to the checks, such as entering hours.
To avoid this, if you already put a lot of work into the paychecks, then instead of reverting you can reset each tax. To to that, Click the employee name and then when the Preview Paycheck window opens, reset the taxes in both of the Employee Summary and the Company Summary tables. To reset them, click on each tax amount (which will be 0.00) and delete it and tab out of the field. When you see "(adjusted)" disappear from the table title, then all of the taxes have returned to standard calculating mode.
