I've had a hell of a time with this today.
Yesterday I did some organizing, correcting metadata of around 3 years worth of collected music.
This morning however, I noticed it had only changed the metadata, and some tracks had been automatically re-organized under the new metadata, but had reverted to the old metadata!
This resulted in some broken links and required a lot of work to correct it.
I have no idea what happened, I haven't done anything in the settings recently.
I'm sorry I can't be more helpful, but I almost certainly encountered a glitch along the way, but it's too difficult to diagnose exactly what went wrong.
So today I went about trying to fix all the broken links and reapply the reverted metadata.
And then I noticed that the folders weren't reorganizing when I changed an album/artist tag within MusicBee.
The setting for auto-organize is still checked, nothing has changed.
Curiously, on the 'organise library files' window I changed the 'on drive' field from 'C:\' to 'E:\' (My music folder is 'E:\Music\' and this causes the program to freeze and requires task manager to kill the program.
I think there might be some weird clashing happening inside my settings file.
The only way I can reorganize files with changed data is by unticking auto-organize and doing it manually with CTRL-R
Here are my settings if they're any help:https://drive.google.com/file/d/0B9DFPZBPKp6AeXhBbV9mUmIxUTA/view?usp=sharing
I should also note that I've since updated my Musicbee just in case that helped, but it hasn't.
With that in mind,I've noticed some extra oddities, but it might be to do with recent changes made to the program.
Before, I was able to drag files into MusicBee.
If I held control, it added a copy of them and organized them appropriately. If I didn't hold control, it added them as a direct link to the file, no organizing.
Now if I hold control, it's no different to when I don't hold control. Also, it moves the file from it's original location in the re-organizing instead of copying it.
I've tried all sorts of settings, but I can't restore the original behaviour...