Just another possibility here, as I find this to be the most common.
It may help to read that letter again, as there is a vast difference between "filing" your taxes and "paying" your taxes. Also, just because the state may have accepted your e-filed state return, does not mean they agree with it as filed. Maybe the state found an issue (such as unreported income) then amended the tax return "for you" resulting in you owing additional tax for which you are being billed.
