Boxes failed to detect that my boxes are in panels. I found the old committed workaround from #1093550: Replace "Edit" text with Contextual Links, and considered re-opening this issue there... but it seems like my problem is actually from an update in Panels or Ctools or similar. Instead of the "panels-content" class that the JS is looking for, I have "panels__content".

Attached a one liner to detect either parent class. Maybe this is the universe's way of telling us to do this detection properly?