I figured it out. I'll occasionally dump files into Mixmeister for sound testing and that program was writing 'popularity' and 'key' into the tags, causing them to corrupt. I tested with a single clean file, turned off the 'iTunes Update' option and the bad ID3s are no longer corrupting.
I use the same program as part of my workflow before importing into Rekordbox.
6,000 corrupted MP3 file tag
Removing the "Popularity" field de-corrupts the file, but also, takes all other tags with it. Do you have a way to remove this field without nuking the rest of the tags?
I don't really fancy re-tagging 6,000 files. lol
have you tried mp3iags with hammer 4?
YES! This actually works.
Under the 'hammer' icon, choose this option:
It immediately restored the v2.3 tag. Wish I had known this before I spent hours retagging everything.
I assume none of the options actually re-encode the actual audio in the file?
From some quick testing, it seems that the "Discard invalid ID3V2 data" option removes the bad data, albeit with an incorrect bitrate tag (320kbs showing as 96/128 etc). Then, if I choose "Remove unknown streams", this too is corrected (file back to showing 320kbs)
However, I wanna make sure I am not missing anything useful on Hammer 4 as there are quite a few more fixes? Seems like a good opportunity to sort my collection even further! 
a good way to use mp3diags is to
- scan the files
- use the filter to reduce the list to just a few if not just a single problem
- fix that problem with one of the hammers or just a single function in the drop-down list
- set a new filter for the next problem
The filters help to see how many files are actually infested with a problem and if that problem should be investigated.
I selected the Discard and then Remove unknown streams options separately. When I used a hammer, it wiped the entire v2 for me.
Edit Just tested with Hammer 4 and it had the same results. I'd feel confident using it for all my files in one step.
It would be great if you or @brandon210 could open an issue/ticket at Mixmeister.
If they sell software that corrupts your tags, they should know and fix it asap.
BTW:
Which software do you use exactly? "BPM Analyzer"? "Express/Studio/Fusion"?
I use Studio v 7.7. I can open a ticket with them.
They actually released 7.8.0.1 not so long back. Update out of the blue!
Anyway, that's the version I use, and it's still an issue. Shall also raise a ticket. Thanks for this thread Brandon. This has happened to me a couple of times now, I was convinced it was Rekordbox initially
Mixmeister is basically ignoring the issue. This was their reply:
"Thank you for bringing this to our attention. Based on your description, it appears that the "Update music files on my hard drive with Library Settings" option in MixMeister Studio is affecting the ID3 tags in a way that causes compatibility issues with other software. We understand the importance of data integrity and will pass this information along to our team for review.
In the meantime, we recommend keeping this option toggled off to prevent any potential modifications to your ID3 tags. For existing tags that have been affected, using a tool like MP3Diag to resolve the issue is a practical temporary solution.
We appreciate your feedback and are here to assist you with any additional questions or concerns."