I agree that he would not gain the additional attack from the short sword of speed, but not because it does not fit into the base attack bonus progression. I agree with you there because the haste effect specifically says that it does not stack with any other effect. Therefore two-weapon fighting granting an extra attack from that would be granting an extra haste attack, which the haste rules prohibit. On the other hand, a monk using flurry of blows is making three attacks at his highest base attack bonus, not his highest attack bonus. To quote the SRD for Greater Flurry: "Greater Flurry
When a monk reaches 11th level, her flurry of blows ability improves. In addition to the standard single extra attack she gets from flurry of blows, she gets a second extra attack at her full base attack bonus. "
This says that both extra attacks are using Base Attack Bonus, not Attack Bonus. Is there an errata for this that I am missing?