Dont buy a car kit!

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Can anyone explain the following?...i purchased a car kit, and had it profesionally installed. At first it was perfect, my xda could sit in the cradle, with screen active, and if a call came in, my radio would auto mute. Perfect!.....but then..i noticed that the microphone would only work with the phone..no others apps [notes, fonix setup,] could access the mic. Then, about two days later, when i put the xda in the car cradle, it would mute the radio whenever the screen was active. I then realised that if i moved the xda slightly, mute would work as before. This points to some physical problem with the connector.
Im using a rom from jeffs kitchen, 3.17.03 and radio version 4.21.00
Has the car kit damaged my connector?...I have seen this mentioned in a thread by a developer?....is there any solution?