All projects are affected; maybe it’s a hinky Scrivener preference or something? By the way, I’ve sent Astrid The Help a zipped version of a project with prologue, epilogue, chapters and scenes as you requested, for your video tutorial on compiling a novel with prologue. But I’ll also send that to the Mac help address, with the subject line “Project for Keithvin”.
Edit: I’m suggesting, really, that the preference may have gone rogue rather than being originally bad (though others seem to be having problems with compiling for PDF too).
Is there any way I can send you my Compile sets, including the native ones and the ones I’ve added?
I have been using Scrivener heavily in the last few months, with up to a dozen separate projects open at one time, relating to one book I’m researching, and to various articles I’m writing and other people’s work I’m editing.
Edit again: Another reason I suspect pref hinkiness is that running Cocktail a couple of times, emptying the Trash and restarting briefly solved this the first couple of times it happened, though not on recent occasions.
Edit furthermore: Trashed the prefs. Made no difference.
Then I went back and searched the Library for
com.literatureandlatte.scrivener.plist
and trashed the resulting preferences. But when I reopened Scrivener and went to use the Compile, there it was again:

So it’s not the preference.
Edit further: I now think the main problem is that Scrivener is not saving the Compile settings.
I saved the 6x9" settings (can’t remember the mm size offhand) in the File/Page Setup menu. When I compiled using the CreateSpace-sized compile set I’d made, I ticked “Use Project Page Settings” in the Page Settings pane, and changed the Formatting pane to tick the “Level 1 (document group)” level’s Text box, and to delete the “Chapter <$t>” in the Section Layout part of that pane.
I compiled and it was fine. Then I went to compile it again, and it had lost all these settings, again.