There's probably little that can be done about the rotors. Friction
variance around the circumference of the rotor due to pad imprinting seems
to be the primary cause of brake vibration. After that, I'd say the second
most frequent cause is overheating. In either case, keep taking it back to
the dealer for servicing under warranty. After the warranty is up, perhaps
try some well-regarded aftermarket brake products and see how they fare.
The compositions may be different, so it's possible things will change.
Of course, that change could also be for the worse.
There's a TSB on '07 Santa Fes for installing a washer between the outer
axle joint and the bearing to rectify a snapping noise when shifted from R
to D or vice versa. Not sure whether this can be done to the '06. And
it's also possible the noise is coming from a different source. It sounds
like the dealer initially found the problem, so now it's time for them to
come up with a more permanent solution.
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