I'm 90% sure it's a file compression issue, I used BatchLZ77 which uses the incorrect compression method (lz10) when the game files are originally compressed with lz11.
I've long switched to a different tool which compresses with lz11, so I'll just rebuild the files with the new compression and see how that turns out.
Also, something your files don't have, while not necessary, if you want your files to be compressed like the original game files, after compressing with lz11, copy the first 4 bytes of the file, paste them again at the start (so they are repeated) and change the very first byte from 11 to 13.