You feel it through the whole bike while moving regardless of clutch in/out.
Do you feel it when the bike is stationary?
I.e., start it on the centerstand and go through the rpms a few times while sitting on it. In neutral, in gear with clutch in, etc.
If it disappears, then you've either got too much knobby on your knobbies, or you have a driveshaft out of balance or something bad in your gearbox (though i doubt that one).