Just to muddle things, I'm not sure I can totally agree with Dandu (though I lean heavily in that direction).
Under AoOs:
An experienced character gets additional regular
melee attacks (by using the full attack action), but at a lower attack bonus. You make your attack of opportunity, however, at your normal attack bonus—even if you’ve already attacked in the
round.
Now, obviously, what this means is that if you are +6/+1 then any AoO you get is at +6.
The TW fighter would get +4/-1 on the primary and +4 on the secondary. So the question would become does the TW fighter do an AoO at +6 or +4?
Consider a monk. A 3rd level monk is +0/+0 when doing flurry of blows (additional regular melee attacks using a full attack action), but according to the above RAW, the monk would make an AoO at its BAB of +3. (One could argue that flurry does not constitute as additional
regular melee attack but as special melee attacks.)
To make matters worse, the FAQ specifically points out (and this is the way we've always played) that if a creature chooses to use a secondary natural weapon to make the AoO then it is at the the -5 penalty of the secondary weapon. Likewise, we've always played that if you choose to do the off hand weapon as your AoO you take all penalties associated for using it off hand.
Hah! To counter again! What if it is not your initiative in the round and you get an AoO? You haven't declared your action. Sure you've got two weapons in your hands but nothing says you're going to use both of them, or maybe you've only got one weapon drawn but you might draw another. What would be your AoO roll?
Perhaps someone has a more definitive answer.