I was just reading this and noticed that both my boots and a measuring tape were both within reach.
I'm 6'2" with a size 10 boot.
The length from the floor (bare feet) to the back of my knee is 21".
The interior height of my boot is about 10 inches.
I can imagine that your smaller boot would be smaller all around (including height), so a 9 inch height on a size 6.5 makes sense.
I just can't see an inch shorter been dramatically different. Sure, there might be more flex due to the increase in leverage, but dramatically more?
Try stiffer boots.