I rebuilt LaunchBox from another hard drive (from which I had originally created this from, for an arcade machine) and I didn't use any files from the old version that didn't have anything in the Playlist View in BigBox AND I now have Daphne and Naomi again multiple times, but no other playlists that are in LaunchBox.
I am updating metadata and will take a closer look at it to see if it is just the clear logos/videos populating incorrectly or if BigBox is only populating these two Playlists/videos.
EDIT: Played with it a bit. I unchecked auto-populate on Daphne and it no longer shows up in playlist view. Went back in and Checked it again and it still does not show in Playlist View. Weird. I also added a different playlist to Platforms and it showed up in platforms in BigBox, but not in Playlists.
I am just going to have to add the playlists I want to Platforms to access them that way.