When you delete Foo, you get a message asking you to delete its folder since it became empty. If you answer Yes, you'll get the result you described. There's also a Remember checkbox there, so I suspect that you had it checked when you last answered this question and chose to delete. This option, as all other similar Remember options, can be reset under Options | Misc | Messages.
Actually I don't get any message.
I looked in Options:Misc:messages and I haven't found anything like "delete the folder", neither checked or unchecked.
Is it there another place where I should have looked?
Anyway there's more than meets the eyes: I discovered that it all depends on the sequence of events.
As soon as I get a repeatable "recipe" I'll report it.