What does your run run the default command: Go REFRESH=source That should updates the file display + folder tree, while other commands may only update the file display.
Preferences / Folder Tree / Options / Fully populate contents may be worth a try, although I think it would only matter here if you were doing something unusual.
Does the file display update to show the new folders automatically, or only after you manually refresh it?
The change notification debugging steps might reveal something.