One of the things I have found in the past is that sometimes with large batches of files, the Zune software does not always seem to see the changes. For example, I may tag several albums at the same time but 3-4 tracks may still look unchanged. In those cases, I will edit and/or save those tracks for each individual file.
I have found that with mp3Tag, if large batch changes are not working as expected, you can often improve your results but working with smaller groups of files.

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