Mp3Tag reads the tags in the order Ape->ID3v2->ID3v1.
So this might be a possible reason if your tags are not in sync.
Have a look at File->Options->Tags->MPEG for your settings in Read and Write.
If you have different content in ID3v2 and ID3v1 you can observe that in enabling and disabling the read-option. I.e. to see only ID3v1-tags just have only this enabled.
Normally Mp3Tag puts ID3v1 and ID3v2 in sync if both are enabled to read and to write and you save the file again.
But there be other reasons. The file can be corrupted, which does not always mean that you cannot play the file or all software shows a problem.
Check your files for errors: