ITunes 12.1.4 loses song locations and isn't properly reading tags cleaned with TuneUp

I've been trying to organize my library lately, including using TuneUp for assistance. I'm on Windows 8.1.
As an example, I imported from a CD I own, but didn't like the iTunes-supplied tags, so I used TuneUp to move to the correct version of the album. iTunes recognized the change and was happy.... for a short while. The next time I started iTunes, it couldn't find any of the tracks (exclamation mark). Looks like iTunes moved the files based on my tag changes - which is fine, but it didn't update itself with the new location it moved them to?? When I locate the file, it works - except for some reason it doesn't ask me if I'd like to to search that location for all files in the album.
So I tried something else - I removed those songs from my library, and re-imported the folder. Despite the fact that all the songs are fully tagged (eg. right click in Windows -> properties -> details shows artist/album/etc...), iTunes placed them under Unknown Artist/Unknown Album.
Unfortunately, it's not just 1 album, and not just from CDs. I'm having the same problem with tons of tracks that I've either purchased elsewhere, downloaded live versions, etc.. and shortly after I tag them, iTunes loses track of them.
But it gets worse... even songs where I go one-by-one and tell iTunes where they are, it soon loses track of! It doesn't even move them again, it just forgets where they were!
So organizing my library has basically become

What format are these files in? For mp3 files iTunes works best when there is a single ID3v2.3 tags. Multiple tags can cause issues. That said if the library isn't saving properly there may be something else going on. Backup your library then try deleting the hidden file sentinel from inside the iTunes folder. This should force iTunes to run an integrity check on the database which may improve things. Also look for .tmp files in the main iTunes folder. If you see any of these it indicates that iTunes is having trouble when it ties to save its data files, which might be why you have the current issue. Excluding the iTunes folder from any real-time AV scans may help.
Does TuneUp connect to iTunes to make the updates, or do you have to "persuade" iTunes to notice the corrections afterwards. As a rule iTunes doesn't automatically detect tag changes made by third party software until it has some reason to re-read the tag, such as during playback.
Almost forgot, I have a script called FindTracks that might help reconnect things that are broken.
tt2

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