Nebraska Tax on Retired Veterans Pay

I do not pay state taxes on my Nebraska Military Retirement Pay. However, I did have them take out $90 each month to ensure I do not owe any state taxes when the time comes to file both Federal and State taxes. When I enter my 1099R for the amount earned the program still has me owing money for State. Where my refund should show the $1080 that I had them taken out of each month pay, it shows that I owe money even though I had a large sum for a refund prior to entering the numbers from my 1099R. Any help in rectifying this situation would be much appreciated. Thanks, Dwaine