Yep....mine does it too....dieseling....when I shut down with the kill switch like the book says to do. haven't noticed it if I shut down first with the key. Mine is a '05 883.
Pete

 

You could have a lot of carbon built up in the cylinders thats still glowing when you shut the bike off causing it to diesel. It will still light any fuel going into them. Run some seafoam through it and it should stop. Put about an ounce to two ounces per a gallon of gas for a tank for and see if it helps.

 

Mine used to do that a bit, but it wouldn't be for 1-4 seconds, it would pretty well just chug/kick once, and be done. I don't think it has done it once since my Heavy breather. I guess since I just have more air in the motor, no fuel is left over.