Please read this Turbo Tax link, written by Daniel that fully explains how to report income to both states.  The important thing here is that you will complete the RI non-resident return first. Here is a summary of his recommendations.

1. "After you have prepared your federal return completely, with the W2's property recorded, prepare the Rhode Island nonresident return first.  
2. Then, well into the Massachusetts return, you receive a screen entitled About Your State Wages.  It asks you if the state wage amount is correct.
3. In the next screen Massachusetts Wages, you are asked if you only want Massachusetts wages transferred into the program.  You will click Yes.  This should remove the RI wages from the MA calculation. 
4. Then, when you get to the Taxes paid to Another State, you re-enter the amount of income you earned in Rhode Island, and the amount of net tax you paid.
5.  Don't forget to input the box 14 RI SDI amount (if any), because MA allows a credit against those payments as well."
6. From what I have read, RI will tax all income from both spouses but you will receive the taxes paid as a credit on your MA return.

Thanks Dave!  I went back and made sure I did as you mentioned above.  I guess the problem comes when MA's Allowable Credit shows as $1200 less than what was paid to RI.  If I redo the states and file separately, my wife's RI return shows a $1400 swing from owing to receiving a refund and our MA returns show the same total refund.  I find it hard to believe there is that much of a difference in the RI return due to filing status.