Actually, it’s not a Scrivener-specific issue; this is a known bug in the current betas of El Capitan (the print preview is also flipped in TextEdit; the headers are fine when printed in TextEdit but that’s because it doesn’t override the standard header/footer code). There are bugs across the current 10.11 betas whereby text appears upside-down in various context (e.g. Safari’s search bar on occasions). All drawing uses Apple standard methods, and the header and footer overrides in Scrivener are the standard way of providing custom headers and footers, so this is firmly an Apple bug. I have reported it to Apple, so we just have to wait for them to fix it in an upcoming beta.
No need to apologise! I’d much have a bug report repeated 10 times than never see it at all! If you find any other problems with El Capitan, please let me know. We’re gathering a list so that I can fix them before release. It’s just that right now a lot of the issues are down to the beta state of El Capitan, so I have to wait for it to get closer to release so I can see what Apple fixes and what I need to find workarounds for. (They better fix the upside-down text thing, though, because there’s no workaround for some aspects of that. I can go back to an older method of creating the headers so they don’t print upside down, but there’s nothing I can do about the print preview… So right now I just have to wait and hope they address these issues.)
I’m trying to get a beta out in the next few hours that should fix this, by the way, so be sure to check the “Beta Testing (Mac)” forum a bit later on. I’m just finishing up a few things before uploading it.