Comments neither threaded nor flat. HELP!

Set up a site for my wife:

http://www.pinkbeemission.com/

Based on the SubtleFlux theme, version 2.9.2. Trying to get comments either one way or the other (preferably flat). View the carnage here:

http://www.pinkbeemission.com/?p=1481#comments

Some are threaded, but all the ones at the end are flat. Whuh?

Modifying the settings under the “Discussion” tab doesn’t seem to have any effect. Any insight appreciated.

Thanks!
-Matt