I'm not sure if this is what you're talking about or not, but I'll give my impression.
I have an '08 SERK and as you all know it's a rubber mounted motor/trans/swingarm etc.
At idle there is the normal motor vibration and the mirror will jiggle a bit too. Once you let out the clutch the bike does a complete smooth out and I've not felt anything this smooth since my wife's.... Well you know what I mean.
I rode this bike many miles and then one time going down a hill at somewhere in the 40 mph range for some reason I pulled in on the clutch and let it coast a bit. As soon as the motor hit idle, moving or not, the idle vibration that I have at a stop light came back. As soon as I re-engaged the clutch the motor smoothed right back out. I tried this at different times while riding and at idle rpms I always get this vibration.
So depending on how long you're holding in the clutch between shifts or if it's just a once in a while happening, this may be your vibration.
If not, all the other guys with the exhaust hitting here or there, loose motor mount etc, could be something to look at.
Good luck and let us know what the dealer has to say.