S Corp electing to pay taxes at the entity level

[DRH3564]

If an S Corp elects to pay taxes at the entity level on its state return (Georgia allows that), shouldn't the amount of taxes paid on the state return in TurboTax equal the amount of taxes that appear on the "Taxes and Licenses Smart Worksheet" on the line "State franchise or income taxes" on the federal 1120S? 
For the past several years, TurboTax has a smaller value of state taxes paid on the 1120S than what's recorded on the state corporate return.  I thought the two values should be identical.
If anyone could clarify the reason for the discrepancy, I would welcome it.

As FYI, we use cash basis, and all taxes paid are paid in the same tax year.  There are no timing issues.

[ThomasM125]

Assuming the state taxes are deductible on the federal return, they should appear on line 12 of Form 1120-S. You have the option of listing them in the worksheet you mention or directly on line 12. Ideally, the state taxes are calculated and posted to the income statement used to prepare the federal tax return, as they are needed in calculating the federal tax liability and to allow for the state tax return to then be prepared, as it works off of the federal return. One reason the state taxes may not appear on the federal return is if you file your return on a cash basis, wherein the state taxes are likely paid in the next year and therefore not deductible on the federal return in the current year.

Without knowing specifically what taxes are missing, I can't say definitively if the state taxes listed on your federal return are deficient. However, since you prepare the federal return first and then use that return to prepare the state return, you may have to review the federal return after you complete the state return to insure that the state taxes originally deducted on the federal return agree with the actual state taxes calculated "after-the-fact" on the state return. 

[DRH3564]

Thanks very much, Thomas, for taking the time to write.

After doing some digging, I believe it's the QBI deduction on the federal return (which does not flow through to the Georgia return) that causes the discrepancy between the two returns.