I've encountered a similar problem by accidentally equipping "Unarmed" in the same Group as a one-handed weapon. The program (correctly, but perhaps non-intuitively) interprets that as meaning you plan to fight two-handed, with your off-hand being an unarmed attack. Once the character sheet prints out, though, it just shows you with a much lower attack than is right if you were only attacking with the one hand, and there's no notation about what's going on.
Tricky stuff.