Usually a college student is the same residence as the parents. If he is only in MA for school, he is not a resident. If his license, voting, etc is PA, he is a PA resident. MA is nonresident, his days there do not count when school related. When you file nonresident, the questions about other state income should go away.
MA taxes earned income (salaries, wages, tips, commissions) and unearned (interest, dividends, etc) income at 5% with some exceptions to capital gains.
A 1099-R that was transferred with no money taken is not taxable. It should be marked as code 4 inherited along with a rollover code. When you answered the questions after entering the form, you had to select that you rolled it over instead of cashing it out.
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