You're flip flopped on what the 1040 indicates.  🙂

If you DON'T want to $3 to go to the Presidential election fund  the 1040 should NOT have the boxes checked.    The 1040 box being checked is a YES to the $3.   

Not a software glitch. Works fine. 

Test it out by marking Taxpayer yes on Info worksheet and Spouse No on info worksheet then look at the 1040.