I have noticed a few times now, when I have 50%+ haste or in a big AoE situation, bot is not accepting commands. it takes 2,3,4 times to press it before it hits a buff like Sigebraker or Rampage.

Have you added buttons to the box below the question marks? Do you press buttons on the keyboard or with the mouse?

Yes, I have added buttons to question mark and i press it( not click with a mouse).
Sometimes if I time CD's with a small delay (0.5sec) bot will take it, but that's not always possible as the situation can hectic.
As mentioned in first post, in full burst situation, heroism + my haste buffs, bot will skip it and I need to press keys multiple times.