I had the same problem. PhoneControl sets the volue to a pre-defined percentage. Here is how I changed it:
Open /Program Files/PhoneControl/PhoneCtl.Config.xml in MS Word
Go to "MainWindow" and change
I think it was originally set at 20% volume, which is fairly loud in my car. If I was listening to music at 10% volume, then it would be much louder when the phone rang. As you can see above, I changed mine to 5%.