I've got an 06 FLHT with an 05 CVO audio system. I often just run the Aux for my music, so I'm not 100% sure when this problem started (I did change the bars recently). The mode switch on the handlebar is completely inop, but when I tried to use the mode switch on the rear speaker pod the left turn signal lit up (but mode didn't change). I'm going to look over the wiring diagrams in the book for clues but I thought I'd reach out for info here. All other switches operate normally, including the rear pod volume control.

 

I wanted to add some findings:
First, I unplugged the rear mode switch, no change. Also, I pulled my aux cord so the radio switched to FM. If I hit the handlebar mode switch down in seeks a new station, but nothing else operates.