Nothing is "centered" in .mobi document

I compiled a novel and chapter titles and separators for scene changes (#) both go left-justified instead of staying centered.

Any idea what the problem is?

If you’ve typed in the scene breaks and chapter headings by hand, rather than having the compiler generate them for you, then you might just need to check off an option. Go to the Formatting compile option pane and click the “Options” button. You should see a checkbox there for preserving alignment. That will keep your centre aligned text centred, and that should be enough for this project. Do note however that in the future you might want to consider using Scrivener’s Separators compile option pane to insert scene breaks for you, as well as the Formatting pane for generating titles based on the names of items in your binder outline. That’s a slightly more advanced approach, but it can make your creative work easier as you can set aside these mechanical details and just focus on the scenes and chapters themselves.

Thank you! Is there also a place to turn off the flush right margin?

If it is possible at all, it would be in that same Formatting pane. Note the mock editor in the lower half. You can make formatting changes to text, titles and other elements that are generated by the compiler.

Do note however that your latitude of control with e-books will often be greatly diminished. Many e-book readers will choose justification options, line-spacing, font, paragraph indenting and other things for you, many at the behest of the reader’s viewing options. So if you want to experiment with look and feel, it’s easier to do that with the PDF compiler output. Then if the same settings do not work on your Kindle or what have you, it is likely simply just not possible to do.