My experience is limited to importing Flash SWF into Presenter, but I've noticed the same behavior. It looks as if Presenter automatically pads the Flash to give it the same aspect ratio as the PPT presentation I'm importing the Flash into.
I found that if I changed the aspect ratio of my PPT presentation to fit the aspect ratio of my Flash, and then imported the Flash SWF, Presenter kept the original aspect ratio of my Flash. For example, my Flash had a 3:2 aspect ratio. I changed my PPT to 7.5 inches by 11.37 inches. When I imported my Flash, its aspect ratio stayed at 3:2.
So if you want to retain the 16x9 aspect ratio of your FLV files, try changing the dimensions of your PPT presentation to 7.5 inches by 13.33 inches, and then import your FLV.
I can't imagine why this would happen, I would be interested in an explanation for this behavior.