When fighting Irenicus, I used the flail of defending and wounding and could not finish SoA. Irenicus stayed at near death no matter how much damage I heaped upon him. Apparently, when the bad guy has a death speech, the flail screws things up. I had to repeat the battle and did not use the flail once Irenicus was slightly wounded. That worked.

Unfortunately, I don't recall who has death speeches in ToB. I found out that Sendai did because the same thing happened in my first fight with her. I had to refight that battle too without using the flail once it was just Sendai.

Has anyone else had this problem? If so, perhaps something can be done to prevent this mishap in the next version?

While I had Sendai and some other enemies bleeding due to the flail I didn't encounter this problem. Maybe because it stopped in the right moment (or rather, when it stopped the dialogue started...)? Did you try to stop attacking the bad guy with the flail and wait (or use something like... FoA)?

Yes, that did not work for me. I guess I missed the "moment." I really don't know what's up with that, but I just try to remember to switch weapons once major personages are injured by the flail. I have no idea why I'm having problems but you did not.