You should make sure you do the Nonresident state first (NY) so it remembers your situation that you have more than one state. Maybe it's because you deleted your MA and started over, and something broke... So you didn't get the screen anymore... Just guessing!
For MA to not pick up your NY wages would mean manually editing the W2 even if you were to file separately. I am uncomfortable with editing the W2 whatsoever. However that seems to be the solution for some other discussion threads.. I am very hesitant to do that.
However, best of luck doing your taxes!!
