I am also having both the controller issue and the "popping" sound through the speakers of my car.
The volume buttons seem to work, but the play/pause button only works when I hold the button for a second or two before letting it go. Because you have to hold it for a second before it registers, you can't use it to go back or forward through songs. I tried the controller from my Venue Pro in the Focus S with the same results, so the problem is probably with the phone itself and not the controller.
Whenever I have an AUX cable plugged into my car with the engine on, I can here a loud whining noise that I assume is the cable acting as an antenna and picking up noise. When I plug in the DVP, it seems to sort of ground the cable and stop picking up noise even when music isn't playing. With the Focus S, the noise continues when the phone is plugged in and only stops when music is playing. During the short time between songs, music is not playing and there seems to be a sort of noise spike that makes a "popping" sound.
I suspect both of these problems are related and have to do with the jack as jmerrey suggests.