That is a separate issue, there was a bug where the editor css did not work, and that bug was fixed, but this one is a "feature" not a bug. Heading 1 is mapped on purpose to h3 when using CKeditor or FCKeditor (my recollection is that I was not able to easily do the same in TinyMCE).
The reason it was done that way is because most users don't understand about html headings and since we have site title as h1 and feature instance title as h2, the top level title that a user should use inside a feature instance is h3 in order to be structured correctly.
If you need to change this behavior there are ways to do it by configuration, or you can use TinyMCE editor.
Hope it helps,