I gave up and eventually allowed iTunes to just handle the folder structure since I had a dedicated Mac Mini at that point. I would rip CDs and let iTunes convert them to 192kbps mp3s and then manually copy to the Samba share. I had a local copy and a copy on my NAS. This was tedious but I never wanted my entire library to become mangled again.
I moved up to dedicated NAS instead of Samba Shares on a windows media center. The problem with NASes is that if a proprietary has has a logic board failure or raid controller failure you must purchase from the same manufacturer if you want your data. I had a logic board failure and was down for 6 weeks during the holiday season from November 2009 - January 2010. Upon placing the drives back in the NAS in the correct order a reboot of the NAS reinitialized the raid array and wiped all of my music, movies, documents, backups and website starting from 1992. :-((((((
I cried and have spent the better part of 2 years recovering the data from old hard drives and online backup.
I now only buy mp3 from iTunes, Amazon, Google play or directly from the artist or distributor. Most of these non iTunes MP3 markets have an iTunes and Windows Mediaplayer app that adds the music that you've purchased and downloaded into your itunes music collection. All my iTunes purchases are automatically downloaded to the library and copied over to the NAS. Google Play and Amazon purchases require and extra step to make this happen. It's usually just a few clicks to identify the music on their websites and initiate a download to their own app that adds the content to my iTunes library. Google Music Manager and Amazon Music Importer also copies that music to the cloud so I can listen pretty much from any mobile device or computer.
All my music is in the cloud, locally on a Mac and on a Nas so I never have to worry about losing it anymore.
Here's the simple bash script that runs at the top of the hour to copy my music over to a mount on my NAS
5 * * * * /Users/xxx/itunesbackup.sh
cd /Users/xxx/Music/iTunes/iTunes\ Media/Music/
rsync -av . /Volumes/Music/