This is still not a bug. When you add more paddings into each containers, the width if the bar and its containers will become narrower. This would result to a messed up column, the container will display onto the next row to make room for your 100px padding because that is a fixed value.
Why would you add a 100 pixel left padding? Are you trying to position the elements to the left side? If you won't mind, please provide a mock up layout of what do you have in mind so that we will have a clear idea of the spacing and the positions of the elements in your header.