How to restore default iTunes media organization? I have iTunes running on my El Capitan Mac Mini. I have the iTunes Media folder linked to a NAS using NFS. This has worked for me quite well in the past. However after upgrading the storage on my Mac and reconnecting it to iTunes things have stopped working as well.
For some reason iTunes will organize the files in the way it would before. It will no longer put movies in a separate subfolder (which I like actually), for TV Shows it will no longer create season subfolders and most annoyingly it will put all the music in the iTunes Media root folder.
What's even stranger is that when I use a local iTunes Media folder everything seems to working as it should. But when I point iTunes back to my remote folder it resumes with the weirdness. 
Is there any way I can check and restore the iTunes media organization behavior?

Edit: 
I've also tried using a different remote location. Both through NFS and through AFP/SMB. All remote locations had the same behavior. Also tried having the iTunes Media folder local and have the subfolders point to remote locations.
In iTunes, select File > Library > Organize Library and check the second box, 'Reorganize files in the folder "iTunes"'. This should move all of your files into the proper (previous) subfolders.