Thanks to Dave S. For reporting this one yesterday.
There was a bug in the current version (1.2) that manifested when a folder was dragged and dropped to a new position in the tree. Adding a new scene or note to the folder after the move caused it to revert to its old position. This has been fixed.
To install, download the fix from the link below, close Atomic Scribbler if it’s open, and run the installation.