At level five I noticed that the elemental bond was making my bard song do elemental damage instead of physical damage. Just recently I purchased a songbook, and added a couple songs to it. Now when I do a default bard song it is doing physical (bludgeoning) damage again instead of elemental damage. Maybe the songbook default song is different from the character default song, is my theory on why this isn't working as it should, so is not noticing the effects of the perk.
Still an issue. Tested and confirmed that without the songbook the song works correctly, but with it the incorrect damage type is used.