Federal and State Taxes are calculating correctly (I hope - I trust the tax tables). It is only the Medicare and Social Security, as these are based on a percentage, it seems that this would be a simple calculation (the employees in question have not hit the annual social security max). For instance, one employee has a taxable wage base of 3212.80, it calculated SS at 189.86 and Medicare at 44.40. SS should be 46.59 and Medicare should be 199.19. 

As I stated before, the first quarter everything was calculating correctly. Second quarter was off about $55 and third quarter was off $95. This payroll alone is off $71 and about 25% of the employees are incorrect. 

An employee at the call center told me it was because we make changes to the paychecks after calculating, but before submitting; I found that taxes do recalculate when changes are made, so that information was not correct. 

If I have already started the payroll process and have already calculated paychecks, will running the verify and rebuild tool fix the existing problems, or will I have to delete all checks and start again?