Best 'Tags' settings for most readability?

The best settings would be:
Read and delete all tag versions
Write only ID3V2.3 UTF-16

But: load those troublesome files into MP3tag and see which tag versions you have in those files.
If you see nothing suspicious (like APE) it could also be that some of your players rely on their own background data and overwrite the tag information.
And in general: check the files' integrity with one or more of the (freeware) utilities foobar2000, mp3val, mp3diags.

But this is more or less the advice I gave you in Is this how opening and saving files work?