I know parenthesis means they're muted but what does the white background of the note mean? They're not showing in Rocksmith. Is there a way to toggle them on?

A gem whose fret number is in parentheses is a ghost note. This is used for different purposes, but the chords won't show up in game this way. To make them normal chords, you can select them and toggle the ghost status with CTRL+G (or use "Toggle ghost" or "Remove ghost" from the "Note>Pro guitar" menu).

Thanks! I just went through and toggled off the ghost notes and then ctrl+M to toggle on palm mutes to create a similar effect.