iTunes isn't saving ID3 tags or syncing cover art (Windows 11's Fault or iTunes?)

I'm not sure if this is something that happened because of Windows 11 or whether this is a bug that just hasn't been caught yet within iTunes, but ever since I upgraded, I have noticed that ID3 tracks don't seem to stick to my Apple Lossless files consistently, and artwork is not being uploaded consistently. It shows up in iTunes on my main computer where the music itself is held, but not in iTunes on my laptop when I listen remotely or on my iPhone 12 Pro Max.

This is happening with my vinyl rips, which is the primary way I get music into iTunes. I encode them into Apple Lossless files, then I use either Tagscanner or MP3Tag to tag the files, but when I go to sync everything (or sometimes even before), iTunes automatically jettisons everything I just did in the tagging programs and goes back to the ripped filename.

For instance, I import a WAV file titled JohnDoe-04.WAV. The converted Apple Lossless file is called JohnDoe.m4a. I take it into Tagscanner and pair it up to an album. I got back to iTunes to update the library, and right before my eyes, it changes back to JohnDoe-04.m4a. Everything I did to it in Tagscanner is just erased.

I started doing all my conversion and tagging in iTunes to save me an extra step and to be able to use Apple Lossless, but if this keeps up, I'll be going back to my old way of doing things and only using iTunes for adding music to my library while I do the conversion and tagging in other programs.

Are there any ID3 settings specific to Apple Lossless files I should or should not be using, or is there a standalone tagger that can handle Apple Lossless? The problem seems to happen more often when I use Tagscanner than MP3Tag, but it happens in both, and I can never tell which files will do it.