You know, I had begun to suspect that it is a timing thing as well. One thing I have noticed is that instead of simply tapping the green "answer" button when receiving a call, if I press and hold it for a couple of seconds I seem to avoid the "failure to mute" issue almost every time.This is usually due to the STS Bluetooth not getting the mute instruction from the phone. It can be a metter of timing. Have you tried answering the phone by pressing the VR button on the steering wheel? I find it easier and it may change the timing of communications between the car & phone.
The Nav firmware upgrade is well worth doing. I'm convinced the Bluetooth, VR & Nav system work better.