Chevy Avalanche owners experienced something similar... with the bug deflector installed, it changed the air flow enough to cause the windshield side moldings to vibrate/flap in the wind. The fix was to install the double sided tape under the windshield side moldings.
Might be worth checking out, even though a bug deflector is not necessarily involved; it does sound like the change in wind direction does create the noise/vibration.
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