iTunes Corrupting Library File on NAS

Hi all. This will probably end up being tl;dr, but anyone who thinks they might know an answer, please help.

I have my iTunes library (the media itself) on a Synology DiskStation DS1812+. Up until today, I've had my library files on the local Mac mini, I moved them to the NAS today to see if that helps solve the issue I'm having. I'm running iTunes 11.1.1 and Mac OSX 10.8.5 (not being at 10.9 is another iTunes problem for a different discussion). I should also mention that I have eight 4TB drives in the Synology and my iTunes library has Music (7,500 songs), Movies (1,100 movies, most in HD), and TV Shows (4,700 episodes, many in HD). My Mac mini is acting as the HTPC and it's connected via HDMI to the living room TV.

In the past few months, iTunes has started to scramble around my files all over the iTunes Media folders. I'll find a song or a movie inside a TV Show season or I'll find a song listed in the Movie list. Sometimes the artwork will change to the song, but the original file using "Get Info" will show what it should be. There doesn't seem to be any rhymn or reason to it. Also, looking in the iTunes Media folders and there will be stray TV Show episodes inside music folders or three movies listed like they were part of a TV Show (01 Name of Movie, 02 Name of Movie) in the root folder of TV Shows. Sometimes TV Show episodes will migrate to an Album folder. It's really driving me nuts!

I just erased and rebuilt my iTunes library in June and don't really want to do it again if it can be helped. One of the reasons I erased everything in June was to try and solve this issue. I've even looked at switching to Plex or something like that, but that would involve so much work that I want to make sure I'm not missing something with iTunes before I take on renaming all these files to work with Plex. Anybody with any ideas would be great ! Thanks!!