It seams that in my case Scrivener does override my font (Lucida Grande) with Optima, even if I configured it to replace the font with Lucida Grande in Compile-Formatting.
So shortly, the override from Compile does not seam to work for me. Any hints?
Make sure that you’ve adjusted the font for all the appropriate document types and levels. Each row in the formatting pane of compile can be set differently, so just click through them (or at least all the ones marked to included “text”) and make sure the font is right for the body text.