I'm having a similar issue. MA keeps pulling all of my 1099 income trying to tax me 5% on my ENTIRE income. I am a NY resident and I didn't have that issue with any of my other state returns. I should owe MA a couple of hundred dollars and its saying I owe thousands. All of my income is 1099 and I cannot find where to say this 1099 is to x state instead of this one.