" If I set the current value of my IRAs to $0 all of this pension income goes away and the refund increases to the correct amount. "
It seems you have found the workaround you need, if it does not mess up your Federal tax return.
I have a similar issue with a Roth conversion (not TurboTax),
I am obliged to set the year end value of IRAs to zero to get the correct result, even though it is not a true statement. I don't think this setting goes through with the e-File dataset.
