By default, when you set the option to Move files from Source to Destination when such files don't exist on Destination (under Decisions-Files settings page), then it will only Move the file and not the folder. The setting doesn't say "Move files and folders from Source to Destination" - only files.
Empty folders are treated under another set of rules (Decisions-Files > Folders).
Empty folders are treated under another set of rules (Decisions-Files > Folders).