So this is how I have always done it:
1) Create folder on desktop, e.g. "New Album" that contains (for example) a track called 01.mp3
2) In Win Explorer I drag the track 01.mp3 from that folder into MM5
3) The track 01.mp3 gets automatically moved by MM5 from the Desktop/New Album folder into my music folder (as defined in MM5) and the 'New Album' folder would get automatically deleted from the desktop by MM5.
But now what happens is that as well as the above steps, my actual Windows Desktop folder (C:\Users\Myname\Desktop) gets deleted and I can't access my Desktop anymore within Windows. I have to go to my Recycle Bin and restore it to Windows.
If I untick 'Delete emptied folders' as you suggest then that does seem to be a workaround and the Desktop doesn't get deleted. I guess I can just manually remove the empty folder from my Desktop but I've never had to do this before. Don't know if this would have any other side effects, like I could end up with empty folders left behind during auto-organizing? Just seems strange that it's only started doing this since the most recent update.
Also, the checkbox for 'Delete emptied folders' is always greyed out and unclickable unless I first untick and then tick 'Automatically organize files (during scans or edits)':
Is that how it should be?