I have version 2.5 and, sad to say, I just never took any notice of how the books were sorted in my reader collections. I was only focused on having them in the correct collection folder.
Now that you have brought this up, it is something that I will have to check out the next time that I set up the collections. (Later rather than sooner as I have just reloaded my Reader.)
Maybe someone will chime in and give us a hint
