I'm sure you're right. Reporting what I've found so far in case it sheds any light....
I have just used MP3TAG, Exiftool and something called Cue Splitter to extract what I believe is all available tag information. Cue Splitter gave the most comprehensive view including "private" ID3v2 tag info. not visible (easily at least) in the other two tools.
I've just checked one of the files in question so far.
I compared field by field in Excel for the phone version of a file and the server version. The only differences were in the order that the tags were retrieved by the tool and in the value of one tag called TCON. On the phone version this had the value "Alternative" and on the server version "20". The separate Genre tag has a value on both of "(20) Alternative".
I know that this file has not been changed on the server since it was synced to the 'phone unless something on the server (e.g. Audiostation or Plex) has suddenly decided to do this. The file modification date on the server is in 2014.
It looks to me like there's something else going on here, but I'm not sure what yet.