The voice activation for song control stopped working with 3.1.2 while connected via USB in my car. Voice activation continued to work fine for phone calls while connected. I had no issues while it wasn't connected in the car.
I found the solution this morning. When the iPhone is connected via USB, the songs are controlled from the head unit, if you open the iPod app, a white screen that says "accessory connected" appears and no playback options are available. However, it has a
Passenger Control mode. To activate it, I push and hold the
Mode button on the deck for 2 seconds. The music can then be contolled from the iPhone as well as the deck. I put it in passenger mode this morning, and voice control for songs worked fine.

I was having to unplug the USB whenever I wanted to change songs via voice activation since updating to 3.1.2, and that was annoying.