I have been using this plugin for a while now and it has worked great so far, but after the last update it is not ordering the folders properly.
When I upload new images to the root directory and then open the drop list to select a directory to move them to the directories in the list are not rendered in alphabetic order as they were previously reflecting the file system.
Each place where you can view the list of directories is now different, the closes match to the file system tree is the select list to display all images in a specific directory.
In the change log it says that the way the directories are displayed has been fixed twice with recent updates, yet here we are all having similar problems with the thing not rendering directories properly.
The fact that the OP started this thread 2 months and 2 weeks ago and the author has not responded does not look promising at all.