There are only two reasons why a bank will not accept a paper check when presented to them.
1) The person presenting the check can not prove they are the payee named on the check.
2) The check is on an account that the bank determined did not have sufficient funds in it to cover the amount of the check.
At this point, this issue is between you, the bank, and the taxing authority (IRS I presume) that issued the check.