With only one employer and 4 different states, It sure sounds like the amounts in Box 16 of your W-2 are being duplicated if the amounts total up to $11,000 more than your W-2 box 1 amount. There are some states that will not exclude certain Federal items, such as HSA contributions, from your taxable income, but $11,000 seems high.
Does your MA box 16 equal your Federal W-2 box 1 amount? If so, then clearly MA taxable income is being reported correctly and should represent all of your income from all the states during the year. Can you reconcile your W-2 with your paystubs?
Can you provide more information about what your W-2 is reporting? Include the states so we can understand your situation.
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