Just in case anyone with the same fact pattern runs across this issue, I figured out how to avoid it.
The software seems to be conflating the issue of a subtraction for U.S. government interest with an addition for federal tax-exempt income which is taxable in Colorado. As I mentioned above, in the Colorado state module in between telling me the correct amount of the U.S. government interest subtraction and calculating the subtraction for U.S. government interest to be $0, the software asks for the amount of federal tax-exempt income which is taxable in Colorado (the Colorado add-back). If I say that the Colorado add-back amount is $0, the U.S. government interest subtraction comes through. If you enter the correct amount of the Colorado add-back when you make the federal inputs for tax-exempt income, the Colorado add-back amount will automatically carry through to the Colorado income tax return - even though you enter $0 on the state input screen.
Hope that helps someone.
