The next step will be the following anyway:
Take one of the unwilling files and load it into mp3tag.
Then select the file and press Alt-T to open the extended tags dialog.
Check if the dialog title says something like ... APE ... (not not only MP3 Vxxx).
If you find APE then your source has written APE tags and they overrule MP3 tags.
have a look at the follwoing thread dealing with APE tags
Mp3tag Does Not Read These Tags...