Another spot to take a look at...
I have noticed a rattle as well from the bags, specifically where the covers rest on the tail portion. The trim next to the tail-lights (black in my case) has a series of raised "bumps" that the lid rests against. Since it is plastic on plastic, it buzzes and vibrates.
I found a sheet of self-adhesive felt at a local fabric and crafts store. Plan on installing it on the bag lid side this weekend to provide a bit of insulation between the two pieces.
'13 Vision Tour - Sunset Red
VM1-HPT-DR Touring Cams
ATS (adjustable timing system wheel)
Vision intake filter and spacer
1/4 Turn throttle
D&D Reverse slash-cut exhaust
And of course, a Kruzer Kaddy just because...