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I know you said D3s but I have a D700 and had this same problem. I sent it to Nikon to be repaired and sure enough, it's the hotshoe is loose. If you put your flash in there and there is *any* play at all, it's a loose hotshoe. I hope you get your problem fixed and sorry to hear about it.
It is ridiculous, IMO, that using a Nikon camera and flash together, would result in a problem like this. I had to pay for this repair too.