This condition is most likely caused by preferences not being set to properly apply changes. You can access preferences by pressing the "wrench" icon at the bottom of the TuneUp program window
The following options are available to edit your files:
Unchecking any of these options will force that particular metadata to be ignored when you press the save button. If TuneUp is not applying changes, this is the area to check, First.
How to access TuneUp preferences