Try opening up this thumb screw a bit more? When I move the box from the car with flatter aero style crossbars I really have to open these up big time for the LFD bars. You should be able to fine tune it so the clamp snaps back down good and tight.
Also, in another thread on this topic my cheat to fix the wind noise howl with the box on was to take some foam pipe insulation and fill the gap in the underside of the front bar. Whisper quite after that! Otherwise, they resonate like tuning forks.
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