I figured out what was going on by comparing the state forms with and without the 1099-INT for the federal bonds. My higher income was resulting in a reduced MN standard deduction, and when the bond interest is added to the federal return, my income is a little higher, which made the MN standard deduction a little lower, which made my MN taxes a little higher... even though the full bond interest was being subtracted out.
So, I think it's not a TurboTax problem, it seems this is just how it works in MN. This seems wrong to me, since the bond interest is not supposed to be taxed by the state, but clearly MN is taxing me on it to some extent.
Also, the refund meters were working just fine all along and were updating correctly for both Federal and State any time I edited the 1099-INT fields.
