Not sure if it will fix your problem, but I've noticed that if I edit an ID3 tag in RB 3.x, I need to also click into another text-field box in the same info window in order for that ID3 edit to register. It's actually a bit of a pain, as when I am trying to edit ID3 tags on multiple (dozens) of tracks, sometimes I forget to do this final click and I lose my last edit.
1] Open up the Info pane in RB3 for any track
2] Edit any field
3] Click inside any other ID3 tag box (don't need to type anything, just click)
4] The tag info should now be saved in the .mp3 file
Would be nice to also also have a feature to clear tags, rather than manually triple-clicking or highlighting each one then deleting them by hand... maybe an "X" beside each ID3 category title in the Info pane?