Hi electricowl, and welcome to the forum.
When I get a compile help ticket where one part of the project isn’t compiling the same as the others, I’ll start by comparing the structure of the flawed chapter and its section type to the others.
If you go to
File > Compile and review the list of chapters and documents in the right-hand part of the compile panel, does that first chapter have the same section type as the rest of the chapters? If it doesn’t, that could be the cause of the issues you’re seeing.
To put this another way, if I have a project with twenty-five chapters that are structured as folders and I want all of them to have the same formatting when I compile, then they all need to be using the same section type.
That way, when I click the
Assign Section Layouts button on that main
File > Compile panel, the example text that I assign to their section layout will tell Scrivener what the text should loo like.
Since the PDF’s output seems fine, that makes me think the ePub’s section types might be a the difference when you change output file types.
If you haven’t used the compile tools much, you might want to check out our 4-part series titled “Getting Your Work Out” on the Mac tutorial videos page.
Those four videos will show using the built-in compile formats as well as accessing the compile designer panel to customize your settings. You might find seeing that process demonstrated is helpful.
The Tutorial also has some documents about the compile process. And, Chapters 23 and 24 in the Scrivener manual go into detail on the settings and customization process. You can access a PDF copy of the manual from the Help menu. That is also where you can access the Tutorial.
I personally like using the Tutorial as a testing space for a number of Scrivener features, including testing out the compile tools and options. That way, I can experiment with different compile formats and output files without using my own work. If I get settings wrong in the Tutorial, I can delete the flawed one and get a new copy from the Help menu.