Mail.app Rules Applied Inconsistently
The issue was mine.
I deleted all the existing rules, and remade them from scratch. Some new rules didn't work well at first, but I modified the conditions (adding a condition with a problematic email selected creates a condition based on that email's attributes) and then used the &quot;Apply Rules&quot; selection from the &quot;Message&quot; menu to test their effect.
After a few days of testing, sorting is now almost always correct, and immediate.