In short, you aren't comparing apples to apples. In the normal bar chart view, you are looking at the % of Responders. That is, comparing the number of people in the department vs the total number of responders.
However, in the second chart (the heat map), you are looking at the % of Responses. You are now comparing the number of questions answered by people in the department vs the number of questions answered overall. If one department has a higher # of questions answered per responder, they would have a larger % of Responses.