My friend(a) didn't say anything, I just checked his motherboard to see if I could learn anything from his setup. He has the exact same motherboard and nothing plugged into the 3 pin headers on it, and a PS2 keyboard. I think I left the manual at his house, but I remember it saying those connectors supplied power to the ports. Which is why I thought it weird he didn't have anything plugged up to them.
Edit: I just talked to another friend(b)/downloaded the manual, and friend(c) that was there when I put the motherboard in took off what appeared to be safety caps. Turns out they were there for a reason. Problem solved, thanks for the input, Dias.