Payroll Federal form 941 amount due does not match check computation

@jpcote 

RE: I've see that the amount QB computes on form 941 does not match what QB tells me the check should be 

Where does QB "tell you the check should be"? It sounds like you mean in the Payroll Center, when paying taxes. Is that correct?

Notably, the Liabilities QB will show you are whatever it is you withheld from paychecks (and also whatever the company paid taxes are). It doesn't matter if they're right or wrong or if someone overrode them with different amounts.

On the other hand, the 941 uses the taxed wages - the wagebase - for SS and Medicare to recalculate the taxes due as a percentage of the total wagebase. For Federal Withholding, it just displays whatever you withheld, according to the instructions.

If the difference is small, about a dollar or less, it may be due to rounding accumulations, since each tax amount on each paycheck is rounded to the nearest cent.

If it's larger, there may be something else going on.

Can you elaborate on what you're seeing with more specific details? Which taxes are different? How much are they different?