Well it can be something as easy as the bot being lagged. It has been my experience that lag can prevent OR make the flood protection from doing what it is supposed to. If lagged it does not receive all the 'info' in channel in the specified time and does not detect it as a 'flood'. On the other hand if lagged and a person has typed a lot in channel and then all that info is suddenly 'received' by the bot it thinks it's a flood and kicks the person.