Hey - I'm no guru as you will see from this answer.
I'm thinking that you are using a new version 1.8 or 1.9 and I use 1.7. So I don't know what changes there have been if any, to cause this.
I'm not one for lots of sub-folders, I tend to use playlists and keep all my songs in one folder, so I don't move them around.
But I can't see why you can't move things around as you want.
Maybe try - On hard drive - -- copy / paste into new folder then delete from old folder - try that.
I seem to remember having some trouble with a file once that wouldn't delete or 'something' and I had remove it from my player to do it. But I have a separate player and it's easy to do that in mine.
------
I've just been away to check out my player MusicMatch and what happens when you move things to new folders.
As I thought - when you move files to another location - then go and try to play it in your player - it can't find it 'cos you moved it. The path to that song has changed.
I think maybe there is some kind of safety feature and because the song is in your player, it won't move it because the path will change and then it won't play. You will have to delete it out of your player I think, before you can move it. *Not delete from library*
That's the best I can guess without knowing how it actually works.
Good Luck
