In most cases it is not enough to change the read and write permissions but you also should make sure that the user-id that starts MP3tag is also the owner of the files.
It could also be that the new program starts some kind of background process that accesses audio files as soon as they are modified and so blocks access by other programs. A look at the running processes could provide clearification.
As the old files are also effected, I would think it is an access problem. Otherwise I would recommend to check the new files if they are mp3 files and see if some settings during the generation lead to problems. See
for a list of mp3 checking programs.