Weird issue with em-dashes and closed quotes

I know this topic has been discussed before. I’ve spent the last forty-five minutes hunting for and reading every forum post I could, but alas, nothing helped me.

So! A bit of background:
I’ve been running High Sierra, and an older version of Scrivener. I could type a dialogue string and end it with an em-dash, and it would automatically close the quotes with the appropriate smart-quotes. This week, I upgraded to Catalina, and today I opened up my current project.

The problem:
Quotes following an em-dash no longer become a closed quotes automatically.

Now, here’s where it gets interesting.

What I did to try and fix it:
I went into System Preferences, to the text tab, and added a substitution, as suggested in other forum posts.

It didn’t fix the problem. (ETA: It kind fixed the problem. I missed a toggle in the Scrivener preferences, so now it offers the substitution for replacement. Which is a work around, but doesn’t address the weirdness of the problem.)

I fiddled with Scrivener’s preferences, did everything I could, but that ending quote refused to close. So I created a new text file within the same project and wrote "test—”

Imagine my surprise when the quote closed, just like it was supposed to! I went back to the text file I’ve been working on and…nope. The quote following the em-dash stubbornly remains an open quote.

I tried copying the old text and pasting it into a new text file, but the problem persists. The quotes won’t close following an em-dash.

Help? I’m just about at my wits end here. I have no idea what the issue is, or how to make all the documents in my current project automatically close quotes after an em-dash, not just newly made files.

I found the same problem years ago and noticed Word also got quotes wrong a lot. My solution is TextExpander. I use, for instance the shortcut ;- to get — ”. The result is em-dash + non-breaking space + closing curly quote (I use the AP style-guide convention of putting spaces around em-dash and ellipsis). I use ;: for the same thing with ellipsis instead of em-dash. I always use those shortcuts if I’m closing a quote with em-dash or ellipsis.

I use TextExpander snippets for the correct closing quotes in 'em (them), 'cuz (because), and other words as well.

There are numerous apps similar to TextExpander, of course.