When I'm coming to a stop or slowing, I'll downshift to whatever gear is appropriate for the speed I'm going. That way if I need to take off I'm ready. Also I don't as a rule use engine braking to slow down. As has been said, you want to be in first before you come to a complete stop, and don't wait until you're doing 10 mph to start downshifting from 6 or it will be balky as well. I've found after I stop in first, I can go to neutral (if it's safe to do so) and then back into first with no problem. Having said that, I don't think I've experienced the sounds you're describing.
2014 V-Strom 1000 - Desert Khaki
2011 Burgman 400
2007 Honda Helix
2013 V-Strom 650 - sold