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I have not heard of using Box 1 for the state income to report. When you work outside of Mississippi they still tax you on all your income. Of course they allow for a credit on the taxes that Alabama charged you.
To calculate that credit they should use the actual tax you paid to AL after they complete the Alabama nonresident return and that requires looking at the same income that was taxed in Alabama and Mississippi.
I cannot ever remember not using the actual tax paid and using the tax withheld by the other state.
Whatever they did in the past I cannot comment on but you can always have your returns checked at another office.
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