First of all box 1b is only the portion (or all) of the amount in box 1a that may be eligible for capital gains rates. It is included in box 1a. So it is taxed at a lower rate.
1099-Div Box 12 is tax exempt interest. Even though it is income, it is not taxable. It is not part of box 1a. Only box 1a will show up on 1040 line 3b.
