You need to override the line 6b check box on page 1 of Form 1040.
The IRS instructions for Form 1040, line 6b, are as follows:
Check the box on line 6b if either of the following applies.
Your filing status is married filing jointly and your spouse cannot be claimed as a dependent on another person's return.
You were married at the end of 2011, your filing status is married filing separately or head of household, and both of the following apply.
a. Your spouse had no income and is not filing a return.
b. Your spouse cannot be claimed as a dependent on another person's return.
This information applies to all years of the UltimateTax software.