BTW, I don't see Brass Knuckles listed as an option for Weapon Focus. I don't know if its supposed to be there or not.
Ok, checked into this. It has "Don't Allow Selection" for Weapon Focus selected.
This is a bug, as if this is selected, then it needs to behave differently than it currently does.
In short, there are one of two ways to read RAW in regards to Brass Knuckles and Unarmed Strike:
1) Treat them as different weapons, so Weapon Focus U.S. and B.K are separate feats, and B.K. borrow damage from U.S but the "weapon" you use is B.K. So AoMF Flaming will not make +5 B.K. weapon flaming.
2) Treat them as same weapons and you can stack all except enhancement bonuses from AoMF with B.K. bonuses (so AoMF Flaming works with +5 B.K for +5 Flaming Unarmed Strike)
As it is now, B.K. are a blend of the two ways. to read the rules.
BTW, I'm so sick of these debates on these weapons on Paizo forums. I wish they would just pick a stance, but Paizo has (on many occasions) said they don't want to pick a stance and answer an official response to these questions usually with "it is up to the DM".
Back to the OP question, I can't detect your problem. I've created a character and I see WF improving his attack with Unarmed Strike. But it doesn't improve his Brass Knuckles (due to a bug I describe above.)