As Minous says - You should see Melee: +2 with the two damages listed. Without selecting BOTH 1st and 2nd (both hands) you will see +4 / 1d3+3 with Two Weapon Fighting selected. It sounds like you haven't selected both hands for Unarmed Strike.
Here's a screenshot of the weapon tab - I made a 1st Fighter since I don't have APG.
Huh, I didn't realize that I'd need Double Slice to offset the damage loss.
But I still have a problem with there being no offhand stats.
Here, for example, this is Officer Getskilled, an immortal mountain-biking vampire from the future.
He is a level-six Cavalier, as you can see.
He has Improved Unarmed Strike, Improved Grapple, Two-Weapon Fighting, Improved Two-Weapon Fighting, and Double Slice.
With ITWF, and selecting his brass knuckles, he has an attack of +7/+7/+2/+2 1d3+3.
But if I do it with his unarmed strike, it's still +7/+2 1d8+3.
I have not found a way to add that second attack bonus, or even a way to just brute-force an extra unarmed strike onto the file.
The way I'm seeing it right now, the only way I can make this work the right way is to just rename some weapons and use them in punching's place.