Mp3tag did retag your files. Check the settings and options in Mp3tag and you'll find an option to Remove the old tags and another for text encoding. Lots of things are going on "under the hood" when you do a mass save in mp3tag, take a look at some of these settings and you'll have a better understanding of WHY it works now.
You probably had some ISO encoded tags and some with UTF (Unicode) and now that you ran mp3tag, they are all consistently tagged. Which is always good.
BTW you can remove the id3 v1 tags altogether, they're pretty much obsolete and all modern DAPs can read v2.3, which contain more information and provide multilanguage support via unicode encoding...