After a lot more research I finally figured out a workaround:
During the MA state interview, you can enter the amount previously taxed on the "Taxable IRA/Keogh Distributions" screen. Enter the nondeductible contribution amount under "Other contributions previously taxed by Massachusetts"
I'm not sure why this is necessary and I didn't have to do this last year but at least it worked.
Intuit needs to make the whole backdoor Roth IRA process a lot easier - it doesn't need to be this difficult.
