Its my understanding that the brakes are assisted with an electric pump instead of using engine vacuum. The noise you are hearing is the pump priming to build pressure after the brakes have been applied. So, you will hear this noise upon startup, and shortly after depressing the brake pedal...
I talked to a glass guy about this same issue. His opinion is the glass on newer cars is much softer and prone to chips. He said he has seen this problem across all brand, makes and models.
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The lack of the 3rd row option on the TE is what turned me away and was the reason we purchased a SR5. Yes, the SR5 wallows and dives like the Queen Mary, but its still safe. I think the on road ride is very acceptable for a full frame truck based SUV.
