OK, so now we have your statement that the files have UTF-8 and UTF-16 encoding.
I wonder how you checked that.
One of the truths in data processing is: if all files have the same properties then they should behave in the same way.
So either you do have a different character encoding in the files - this would then explain the different appearance in the player - or they are messed up already because a previous program did not know how to handle the tags. But then they should appear just as bad in MP3tag.
You could also check if you have just ID3 tags (v1 and/or V2) or also APE tags in the files.
Get rid of the APE tags and see what you get.