@sonzoil As @ErnieS0 told you the annualization has to be entered to reduce the penalty. If all of your income lands in December you should be able to reduce your penalty. If you change your mind and decide not to annualize you just need to go back and change the check box from annualize to don't annualize and you're all set.
As for why Massachusetts income is lower than federal it would depend on what type of income you have in your return. Massachusetts has different rules for what is taxable than the federal government, as well as what is deductible.
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