Yep. Happens all the time.
I have at times had trouble resolving the situation until I actually removed the cones and put them back in. Which is to say loosening/moving/retightening the assembly didn't work. I'd take the bottom cones and swap them with the top cones just for drill.
I have not had a recurrence of the situation after installing a one piece top clamp (used stock bolts, no washers, had a mount for the odo machined into the piece). I noted no additional vibration with the one piece clamp. I can't imagine it wouldn't, but you might ask FRP if their clamp accepts the odo. The picture on their site looks pretty roundy on the RH side.
I just got a set of cones from scotts. My imo is they are no good. The cones are too small. When assembled, the metal top caps seat against the clamp. (yes, I used the 'for kdx' additional spacers) Great for rigidity, of no use for bar isolation (which is the point in the first place).
I put the stock cones back in after one ride. If I want my arms to be numb all the time, I'll buy a pumpkin! ;)