So the monk's flurry of blows states that it works like two weapon fighting... which brought up several issues for me between it, and the 3.5 flurry of blows:
And for me, too. The way I see it, the rules are quite easy. But please, correct me if I'm wrong.
Two-Weapon Fighting (Combat)
You can fight with a weapon wielded in each of your hands. You can make one extra attack each round with the secondary weapon.
Benefit: Your penalties on attack rolls for fighting with two weapons are reduced. The penalty for your primary hand lessens by 2 and the one for your off hand lessens by 6. See Two-Weapon Fighting in Combat.
Normal: If you wield a second weapon in your off hand, you can get one extra attack per round with that weapon. When fighting in this way you suffer a –6 penalty with your regular attack or attacks with your primary hand and a –10 penalty to the attack with your off hand. If your off-hand weapon is light, the penalties are reduced by 2 each. An unarmed strike is always considered light.
When fighting two-handed (for the monk, since his limbs are lethal weapons, two-handed means armed or unarmed), you get one extra attack during the round.
Without having the TWF feat, this would, when fighting as an unarmed monk of first level give an attack sequence of -4/-8.
With the TWF feat, it would be -2/-2.
Flurry of Blows (Ex): Starting at 1st level, a monk can make a flurry of blows as a full-attack action. When doing so he may make one additional attack using any combination of unarmed strikes or attacks with a special monk weapon (kama, nunchaku, quarterstaff, sai, shuriken, and siangham) as if using the Two-Weapon Fighting feat (even if the monk does not meet the prerequisites for the feat). For the purpose of these attacks, the monk's base attack bonus is equal to his monk level. For all other purposes, such as qualifying for a feat or a prestige class, the monk uses his normal base attack bonus.
As I interpret this rule, you choose to add an extra attack at the expense of accuracy, and therefore incur a -2 penalty on your hits.
Normal FoB-attack: -1/-1 (BAB = monk's level of 1)
TWF and FoB, without having TWF feat: -5/-5/-9
TWF and FoB, with TWF-feat: -3/-3/-3
x = primary attack, x = extra FoB-attack, x = secondary attack.
As far as I can see, this does not in any way contradict the rules. The phrase "When doing so he may make one additional attack (…) as if using the Two-Weapon Fighting feat" is merely a reference to which mechanics have been applied, and does not state that he is now considered to be "TWF-fighting". He's therefore incurred a penalty-2.
The idea of flurry of blows is simply that you attack really-really super-fast, thus loosing accuracy, but still getting a chance to land one extra strike. The monk is therefore incurred another penalty of -2.
Sor 6 / monk 6 w/TWF and flurrying with light monk weapons or unarmed strikes, whichever way he chooses:
Monk BAB = lvl = +6/+6/+1, but penalty for flurrying yields BAB of +4/+4/-1
Sor BAB = +3
Penalty for extra TWF-attack: -2
Result (I think): +5/+5/+5/+0 (pri/FoB/sec/pri2 – since the Sor BAB is added afterwords)
The result would not be +5/+5/+5/+0/+0 (TWF adds only one extra attack)