I, too, am having the same problem. When users select Heading Large, Heading Medium or Heading small from the editor, it saves as H3, H4 and H5. Going into the HTML one can change it manually back to the desired headings, but it is very frustrating for students who don't feel confident editing the HTML. There must be some code rewriting the headings or those settings for Large, medium and small are in a CSS somewhere set to H3, H4, and H5.
Here is sample HTML generated from using the Heading Large, Heading Medium and Heading small:
<h3>Mammals</h3><p>There are many types of mammals.</p><h4>Mammals that eat us</h4><h5>Lions</h5><p>Lions are a type of cat. </p><h5>Tigers</h5><p>Tigers are a type of cat.</p><h5>Bears</h5><p>Bears are a type of bear.</p><h4>Mammals that we eat</h4><h5>Cows</h5><p>Cows are made of meat.</p><h5>Pigs</h5><p>Bacon comes from pigs.</p><p><br></p>