First off, let me say that I have never used this module so I don't know of a workaround for it. Whenever I have changed ID3 tags in the past, I have used MP3::Info module. You could look into that one, but I do not know if it would run into the same problem.
Have you tried contacting the author of the module to report the problem? Maybe they are unaware of the problem. If you do so, try and provide an example MP3 so they can duplicate the problem. Reporting it as a bug would be the preferred approach so it can get fixed.
Try either sending an email to the author (email address is listed in the AUTHOR section of the documentation), or submit a bug to rt.cpan.org
Brad